Let's Play 'What's wrong with my Transmission'- E46 auto woes

I have an E46 325i wagon that has generally been good to me, but this one is annoying.  I parked it last Thursday without any issues or concerns, had to use the truck for some work-related things this weekend.  I went to jump in it this morning, and it was really slow to turn over, but fired.  I was greeted to basically the entire cluster of EML's lit up for a few seconds, when presumably the alretnator started sending power and all was right with the world... until I went to take off. 

The transmission service light stayed on, and it feels like I definitely am missing some gears.  It drives, but from a stop is dangerously slow to get to speed.  Once I'm at 30mph or so, it drives completely normally.  There is no fluid anywhere that I could see, and switching into Sport/manual mode does nothing at all.  I tried recycling the car on/off without success.  I haven't tried to reset the ECU, but that's my next step when I get home... erm, hopefully. 

Other than fluid replacement, what are my chances that this is just an electronic gremlin due to the battery being drawn way down after sitting?   The car was running perfectly before I let it sit for 5 days, I have no idea what happened. 

You don't happen to have a BMW-specific scan tool, do you? Pulling the code(s) is going to be the most efficient way to diagnose this. That said, low voltage does weird things to modern BMWs - might be worth checking the battery to see if it's on its way out.

I do, just not physically with me at work.  That's the first thing I'm going to do when I get home. 

Reset everything and get it on a charger to get the battery topped off.  Then see what you get.  A low battery causing a bigger voltage dip at startup, etc. can cause some weird stuff.  So I'd want to rule that out before chasing other potential issues.  

BMWs default to 3rd only in limp mode.  Sounds like what you have.  

Can be a bad wire in the tranny harness if not battery related.

Low voltage will trip limp mode. Most require a reset.

Agree with the above.  I recently had my E46 auto at a BMW specialist and they were telling me that when a battery starts to fail it can send these cars into all sorts of a tizzy.  It requires a reset before the car returns to normal, not to mention weeding out the actual source of the low voltage to start with.

Good luck in your search for the answer!

Man, you people are all way smarter than me :) 

Quick reset and she's back to running as normal.  Thanks again!