We ship a lot from our office to freight forwarders. Mostly boxes from 10 to 50 pounds. ALWAYS by FedEx. Have never had a problem, fully insured, clear tracking numbers. I really don't care if they are a bit more that USPS, my peace of mind is worth it.
I've been selling on eBay since 1997 and have feedback in the low thousands. It's gotten really expensive and really tilted toward the buyer but it's still sometimes the best way to sell items. Things got much worse for sellers when eBay made it so they couldn't leave negative feedback for buyers. There were plenty of sellers abusing that but their solution was not the right one IMHO.
You need tracking of some sort, which has been covered. As you found out Media Mail does not offer tracking. You also need to enter that tracking info into your "My eBay" seller's page as soon as you have it so they show it as shipped. Do not click the "mark as shipped" button until you have the tracking info. That tracking is the only thing eBay will trust; they do not believe you if you say you shipped it but haven't entered the tracking info.
Their shipping tool is convenient beyond measure! If your post office is adding postage after you've paid eBay for it that is probably not right. The thing they may not know if it's a rural post office is that eBay has discounted rates for their online purchased postage. So if the counter person at the post office is plunking the thing on the scales and calculating postage in their system it's going to be higher than what you have and should be paying. Now, you need to be weighing your stuff accurately so if their scale says it's heavier than what you claimed then they're right to raise the rates. But I've had them try to charge me more for something I'd paid for online and they were in the wrong.
Media Mail DOES have tracking numbers, and we DID enter them. Didn't matter. Buyer claimed package was lost, EBay ruled in their favor without response from me, and disregarding the tracking information which showed when I sent it, and that it was still in transit in USPS's custody.
The ONLY thing it took for them to issue a refund to the buyer was the buyer's allegation it was lost. Any buyer could do it fraudulently.
I believe that the media mail tracking numbers are for internal USPS use only; can you enter them on the web site and get real time tracking updates? If not then it's not a useful tracking number from the standpoint of what you're trying to accomplish here.
In which case, your second paragraph is false - if there was a valid, useful tracking number, such as is issued with UPS, FedEx, or USPS Priority and Express Mail shipments, then no - the buyer could not just fraudulently claim they didn't receive it. There is still some level of trust involved in the transaction which is unavoidable due to how eBay has their system set up.
I wonder if your post office is just really bad. It might explain the lost and slow packages.
Edit: Did you pay extra for tracking? It might also be that the media mail tracking numbers only work if you've paid for it. In checking the USPS web site though it says the "USPS tracking" is free for Media Mail at a retail location (postal counter) but "not available" for click'n'ship. How did you buy the postage? Online or retail counter?
USPS has gotten more expensive with shipping amounts and their updating of tracking information has gone downhill in the last year or so. I find myself shipping less stuff and using Ebay only as a last resort. I prefer to sell to one of you guys instead. 
I still ship USPS, but only HEAVILY insured stuff.... I sell rarely on ebaY... but when I do I've not had a problem with either the buyer, or ebaY... but USER beware sounds like a plan
In reply to dculberson:
Incorrect. Media Mail has tracking numbers just like everything else. It's not internal, and it does work on their website. And I didn't pay extra for it.
Looks like the final tally is that only 5 out of 12 packages arrived safely.
That's about $700 worth of product I lost and had to refund.
I guess the moral is do not ever, ever, ever use Media Mail, unless you are trying to bleed out in the most inefficient way possible. It would have been much more pleasant to just send each of those buyers a $100 gift. 
I've somehow managed to sell tens of thousands of dollars of stuff without this situation occurring even once. You did something wrong between shipping and entering info into the eBay system or there are employees at your post office stealing packages.
Now that I think about it, the latter seems likely. Maybe soon there will be another big bust of a postal employee with mountains of mail in their home.
In reply to dculberson:
Do you ship Media Mail?
Obviously something is terribly wrong. But it doesn't change the fact that it happened.
BTW, I have continued to ship product since I started this thread using only Priority Flat Rate. Same Post Office. Same products. I ship about 15 per week. Not a single issue in 3 weeks. 100% have arrived safely in 2-3 days.
My answer- no Media Mail.
I forgot...
It was actually only 4 out of 12. 1 arrived with the packaging destroyed, but the product OK. Buyer was cool and accepted it, plus gave me a call to give me a heads up that the package had been damaged.
I think a Media Mail label is open season at the PO for morons to show their azz.
Not saying this is you but back when I was a window Clerk I would look for people trying to rip off the post office by sending things that weren't media and labeling it Media Mail to get the lower rate. You eould be surprised how many little old ladies will I lie your face and tell you there's nothing in the box but books, go in the back open that package up and she's mailing all kinds of pots and pans and whatever else. Yes we are allowed to open packages up and check if they say they're going Media or Library rate
As a regular mailer I will tell you that yes, something is terribly wrong with the USPS.
You have options, use them. Where you don't and you get screwed by the USPS, you eat the mailing cost, eat the product cost, replace and resend (again, at your cost) with a "sorry, my bad" and hope their bad service doesn't cost you your reputation.
Reality, now with extra bite-I-ness.
Margie
In reply to tooms351:
Mine is ALL books. I have thousands, selling 2 or 3 at a time.
But I am definitely not going to ship any Media Mail again.
You'll need to log in to post.
