Okay! This should be all fixed!
Here's what was happening.. for some reason (this is still not determined) our system has been reconfiguring our ftp server configuration file a LOT on most servers.. like every few minutes. It SHOULD only be doing this when somebody messes with anonymous ftp settings (which is pretty infrequently) but something unrelated seems to be scheduling it.
Anyway, these changes would then schedule an ftp restart on the server, which would drop all current connections! And since this was happening every few minutes, big file uploads couldn't finish.
For now we've fixed it by changing those restarts to just reloads, which re-read the configuration file but don't drop any ftp connections. In woody (the older version of debian) apparently a restart wouldn't drop connections.. but on machines upgraded to sarge it now does.
Now we're going to try and figure out why it's reloading so much when it really shouldn't need to in the first place!
But nonetheless, changing the restarts to reloads should have fixed the problem for good!