Is my Airport Extreme corrupting my drives?

Question

I've read a number of Apple Discussions about issues similar, but not quite the same, as the one I'm having. It's driving me mad because I can't pin down what's wrong to find a fix.
The drives I have attached via network seem to corrupt over time. Last year it was the 1TB, this year the 3TB has been acting up (and 2 weeks ago the *other* 3TB was completely freaked out - missing 1/3 of its files -  and had to be wiped (it has the identical content to the 3TB MiniStack because I am resigned to a cycle of wiping and re-installing at the moment).
Example of problem: Currently I have 421 files on one of the 1.5TB partitions. They are absolutely there. When the drive is connected directly to my Mac, I can see them all and it says 421 files. When I put that drive on the network, it says it has 419 files. If I attempt to drag one of the "missing" files from my Mac to that drive, it tells me there is already a file by that name in existence and asks if I would like to replace it. So, on some level that file is being recognized even though via network it's not in the file count, it's not showing up in iTunes, and is not showing up in the Finder.
Last night I was also randomly getting a -50 error when trying to move a file onto that drive via network, and I got several disconnect messages even though the networked drives were all still visible and accessible from my Mac. I've gotten those disconnects randomly before, but not in that number. I'm not getting that this evening, though the file there/not there issue is still with me.
The "missing" files are the last 2 alphabetically (one is a folder, one is an m4v file, both start with Z). When a partition on the other 3TB drive melted down, most of the missing files were in the H's and A's (movie files). I can't figure out a reason for that but it does seem weird. In previous disappearing file scenarios, it's not the same two that are missing now, so I don't think it's a bad file. The other partition on that drive seemed OK.
I've swapped drives (including some not mentioned here), changed the order in which they are plugged in, changed cables, it happened in 10.5 and now in 10.6.8, it's not iTunes because, while it can't see the files, neither can the Finder. The only thing that hasn't changed is the Airport Express Base Station, which makes me wonder if it's corrupting things. Is that even possible?
I ran Sophos on every drive I own - all are clean. I ran Disk Utility on these 2 networked drives and they both checked out fine right now (2 weeks ago the previously corrupted 3TB was irreparable, as were disks before it, thus the constant wipe/restore cycle. I suspect I'm heading down that path again.)
I have been plagued by this for at least 2 years now. Perhaps because I'm trapped in the house from a blizzard, I'm motivated to fix this annoyance once and for all instead of wipe/reinstall/repeat every 6 months. The idea of streaming my movie, tv and music library from the basement (leaving that wire-y mess down there) to my Macbook is nirvana for me. Apple's marketing makes me believe it can happen via Airport Extreme. What am I missing? Am I asking too much from networked drives and would having an old Mac hooked up as a server work better?
Help! :-)
My setup:
Airport Extreme base station 802.11n (3rd Generation) w/version 7.6.1
USB attached drives - AEBS directly connected with NewerTech MiniStack Classic 3TB w/powered hubs, divided into 2 1.5TB partitions. Attached to the MiniStack Classic via USB is a MiniStack v3 1TB drive (the other 3TB mentioned above is an OWC Mercury Elite).
Airport AND drives are plugged into an APS battery back up, so even when the power hiccups here, they don't lose power.
My computer is a Black Macbook with 10.6.8 and iTunes 10.7 (staying put because I like the flip-through-the-artwork feature, and this doesn't seem to be an iTunes problem).

Answer 1

I did discover a way to make all 421 files show up! I made a new folder on the partition giving me problems, and dropped all the visible files into it. As soon as I did that, the 2 missing files appeared. That would seem to indicate a number-of-files limit except for the fact that in the other partition that number doesn't apply.
I had 54 files on that partition, and I copied over an additional 400 to see if I'd only see 419. Once again, there were 2 missing files, but that means I see 452 instead of 454. And weirdly enough, it's not the last two files, but rather the first newly-copied file and the last pre-existing folder that are now not visible. They are still there (as a search finds them) but that's the only way they're found.
I wondered if partitioning caused any issues so I tried this out on my 1TB Ministack v3, and got the same result. again it was exactly 2 missing files (but these were not sequential in the list, one was one of the first added, and one in the middle). What's consistent:
1. It's always 2 missing files (not necessarily the last ones in the list)
2. It's limited to the root level of a drive. A folder that I put 425 items in has 425 items. If I do that at the root level, it shows 423.
3. It only happens when the drives are connected via USB to the Extreme. Since this is something advertised by Apple as a supported use, I don't understand why it doesn't work (I've seen the numerous threads about TimeMachine issues... that is *not* what I'm doing).
I seem to be having a conversation with only myself here, but I'll keep trying anyway. There has got to be someone with an idea of what the issue is so I can try and fix it. At the moment, I'm looking at getting a Mac for a traditional server and warning anyone I come across to avoid connecting a USB drive to an Airport device unless they enjoy losing data and/or re-formatting drives every 6 months.