BMW E39 Odd No Crank Issue

I have a 2000 BMW 540i six speed. Recently the stereo has been intermittently cutting out along with the turn signal indicators on the dash and the reversing lights. I read that unplugging the amp and/or cd  changer can reset this or failing that disconnecting and reconnecting the battery can help. I tried the amp and cd changer with no change so then I tried disconnecting the battery.

I think I screwed up here because I didn't let the car go to 'sleep' before disconnecting the battery. When I reconnected the battery the car wouldn't start - no crank or even click from the starter. All the dash lights come on and the door locks work fine. The battery shows 12.7 volts and the terminals are tight and clean.

Have I fried something or maybe set some security mode? The alarm sounded when I reconnected the battery but shut off when I unlocked the doors.

Any suggestions? Thanks

Still looking for help on this. 

Is it normal for the alarm to sound when reconnecting the battery? It shuts off as soon as you lock or unlock the doors.

I noticed the steering column doesn't move back to the preset position when the key is turned to the ignition on position and the trip counter reads 0.0 which seems to indicate something has reset?

A friend who used to be a BMW tech thought it might be the ignition switch although he hadn't seen this issue before.

Trying to decide whether it's better to try the switch or tow it to a shop to be diagnosed. Or does anyone want a 540i 6 speed for the challenge...

This is going to sound really odd, but flip down the right side sun visor and see if it will crank. If so, it's the ignition switch. I forget the exact reason why this test works, but it had to do with the vanity light in the visor feeding voltage somewhere.

I am of no help other than to say that my 2004 e46 m3, same era/electronics as the e39, never sounds the alarm when reconnecting the battery. 

I know you mention that the battery shows good voltage, but I would either try another one or try starting it with jumpers on and the other car running. These cars are very sensitive to low battery voltage and will start acting weird when connected to one. 

My E39 did really bizarre crap like this when the battery started going south. Replaced the battery and everything went back to normal.

Thanks for the replies - I've tried the sun visor test, no difference and I've tried it with jumper cables to another car.

Sounds like the alarm going off isn't normal then.

Can you turn on the ignition and then try to jump the starter to see if it cranks? Seems like you were having wiring issues, no crank could be EWS issue. Get a scanner on the 22 pin and see if any codes thrown??

In reply to Olemiss540 :

Planning to try jumping the starter, haven't had chance yet. Could try tow starting it too or would that cause other problems? 

I don't have a scanner for the 22 pin port, I'm guessing the OBD 2 port wouldn't show anything?

Like others have suggested, try jumping with a running car. Battery issues can cause all kinds of mayhem even if a multimeter says it has 12 volts.  Many a BMW has been "fixed" with a new battery. It's less to do with the number of volts a multimeter can read and more to do with the load on starting and the cpu seeing the correct voltage.

In reply to gunner :

Already tried jumping from another car with no change. Going to try jumping the solenoid wire on the starter in the daylight this weekend, may also pulled the ignition switch and give the contacts a clean.

Don't really expect much success as I think the alarm sounding whenever the battery is reconnected probably indicates something is wrong but want to eliminate as many possible issues as I can before either taking it to a shop or getting a scanner and pulling codes.

Have you tried locking and unlocking it from the keyless remote? 

In reply to dculberson :

Yep, and the alarm shuts off and stays when you lock or unlock it - with either the key or the remote. So, part of the system at least is working but I don't think it's right that the alarm sounds to start with.

So I jumped the starter solenoid wire and the engine cranks. Switched the ignition on and jumped the starter again and it fired up. That seems to rule out the EWS immobilizer as a problem?

I pulled the ignition switch and cleaned the contacts - no difference, still won't crank from the key. Checked the switch with a multimeter and there is 12v to the starter wire (at the switch connector) in the crank position.

I bypassed the clutch interlock switch, still no crank from the key. I then jumped the starter one more time, the engine fires up but the alarm starts sounding. Using the other key to operate the door lock shuts the alarm off.

I'm thoroughly stumped now as to what the issue could be. I'm going to temporarily disconnect the alarm siren and  hook a push button directly to the starter so that it will be drivable at least. 

Any suggestions?

A little google fu points towards EWS issue. Apparently the ews system on an e39 is a two step process.

1.) Verify key matches EWS system allows car to crank

2.) Verify EWS system matches DME allows car to run.

Sounds like a key sync issue between EWS and key. Need to delete EWS or have someone with INPA resync. This would be confirmed with a BMW specific diagnostics scanner I would think.

I would try and get a copy of INPA and disable the EWS, at least to rule it out. 

Is there a relay that energizes the starter?

Yeah, sounds like key synch issue could be it. Don't have INPA and not really too confident about changing settings with it so I might take it to the local indy BMW shop. 

Not sure if there's a starter relay, I'd guess there probably is - have to do some searching for it.

I had a similar problem, full battery, no crank, no clicking, nothing.  My problem happen around the same time when I had multiple issues.  My starter went out, so I replaced it.  The ABS module went bad (trifecta), so I had it rebuild.  Oil was getting to the transmission connectors, so I had them cleaned up.  After I fixed all of that (over a period of a month or so), then it would not start.  I took it to a shop and they told me that the car would start when power was applied directly to the started; but they could not figure out why the key was not doing it.  I decided that I did not want to spend much money on this at the time, so I hooked up a wire to the starter and brought the wire inside the cabin.  I connected a momentary switch from Home Depot (a couple of bucks) and I plugged the wire into the cigarette lighter.  When I pushed the button, the engine would crank.  Every time.  So I drove like that for a couple of weeks and the car decided to start with the key again.  I did not replace anything.  It has been two years and I have not had this problem since.  I still have the wire connected to starter just in case.  No need to disconnect the other wires on the selenoid.  There are three contacts on the selenoid:  battery power, power in, and power out to the motor.  If you connect to the power out, then the motor will spin but will not engage, so no cranking.  If you connect to the battery power (thick red wire) then nothing will happen.  Connect the wire to the power in (thicker black wire).  The power out wire is a sensor. Ground is provided by the chassis.

Hope this helps.