File corruption/connection issues with NAS storage

I'm curious how many people out there have run across problems with OS X 10.8.5 or 10.9.x when using shared folders from a NAS as the destination?

Specifically, my workplace has several QNAP NAS boxes (2 different models in use at different offices, but I believe the firmware for these is unified across all models). We're increasingly running into issues where a Mac user tries to connect to one of the shares and just gets the spinning beach-ball.

We've already trained users to try all the "tricks" like making the connection via afp: or smb: or cifs: before giving up on it. But my experience is that when none of the 3 protocols successfully pulls down a file directory, I can reboot the NAS and get it to work again. But even when we're not experiencing the connection issue, we've started having a data corruption issue.

I know QNAP is currently having problems with version 4.05 of its NAS firmware, for example, which causes AFP protocol to corrupt data. We've run into this with such things as Adobe Illustrator documents. (User had to zip them up before transferring them to the NAS to prevent them from becoming unusable.) But the QNAP forums say that even for people running firmware 4.05, the "solution" is to simply use smb: (or cifs protocol instead. We're trying that and still running into some document corruption - specifically with JPG or GIF images, where it looks like the very last byte or two are missing from them.

Before I blame all of this squarely on QNAP's products though? My concern is that these issues span most (all?) of the NAS products based on open source Unix variants like BSD or Linux? I built a FreeNAS box with the latest release version of FreeNAS to try out in our office, and encountered such issues as my Mac getting a spinning beach ball and freezing up if I tried to start 2 or 3 large files copying simultaneously. (Copying just one at a time seemed to work properly.)

The Windows machines on our network haven't exhibited any of these issues at all that I know of .... which might explain why you don't see a huge number of complaints about these NAS solutions. Not sure there are enough Macs using them extensively like we do here?