I also use Stamps.com, and have for the last 14 years because of the downtime and unreliability of eBay's shipping/labeling service. With Stamps, I have never had a problem like the one you are having, so there must be something else going on. Most likely, it's not Stamps or eBay -- possibly some incompetence at the USPS (duh...)
Are you aware that Stamps.com can automatically back-post your tracking number right into its slot at eBay so that you don't have to manually upload it? Perhaps you are already having Stamps do this. (You can also have it automatically post the buyer + feedback - a real time saver).
Occasionally the letter carrier may be in so much of a hurry at your mailbox, that he forgets to scan in the tracking # at pickup. This has happened to me a few times, but the PO scans it that evening unless it goes to the regional center, where there can be a backup to cause a validation problem for you. That's when your s/h time might be a factor in getting the scan posted in time. So make sure that you have a couple days of s/h time to give the PO the chance to get the scan done.
If this affects your TRS status you may have had, keep in mind that in the end a TRS status is not that big a deal for a lot of sellers. When I lost mine due to no tracking # on letter-sized sales, it didn't adversely affect my sales at all. About 15 years ago I took down from my office wall that cheesy TRS certificate eBay sent to me.
You say that you enjoy talking to your letter carrier. You might want to let him know how important it is that he scans your outgoing mail every time, and that any substitute carrier is told the same thing. Until then, I agree with @ebooksdiva: Until the carrier scans every time at pickup, it is best to take it to your PO and have it scanned there and give you a receipt. Your round-trip mileage is a deductible expense, and is currently quite generous because of being substantially raised in June.
As much as it applies to your situation, I hope this helps.
Cheers, Duffy
