The problem is that the drive that's connected to the USB port randomly gets connected a couple of times a day, and I don't why it's doing that. I keep getting the "drive was ejected improperly" or something along those lines error message. Obviously, I need something more reliable than that, so I'm hoping it's a bad cable? Maybe the Mac Pro needs a firmware update? Not sure. There was ONE instance of all three drives disconnecting, but that was after waking it from sleep - again - not good. But if it's a matter of just not having it sleep, I can live with that for the time being.
Just wanted to chime in, since I seem to have the exact same problem with my fusion flex. I have connected 2 8TB SATA HDDs to the SATA ports and 1 older 1TB Samsung 840 EVO I pulled from my hackintosh (where it has been running flawlessly). On a side note, I also had a bad experience with a WD Gold, that consistently disappeared on a restart, but reappeared on a cold boot. So I switched to two WD REDs (the slower 5400RPM version) and all is good now (and relatively silent as well). Just FYI.
So now, while the SATA drives seem to work flawlessly, I also got those disconnects with the SSD hanging on the internal USB port. Those issues remain when switching to another drive, and the very same drive behaves well in an external case. I first thought it was some energy saver problem, but it is apparently not, since I also get those disconnects in the middle of a copy operation (leading to data loss!). My greatest fear was that my USB port is broken, but as you seem to report the same, not so sure anymore. And, I get this problems also when the drive is unmounted - and also with Bootcamp! - so it clearly seems to be a hardware issue of some sorts.
And since the disconnects also seem totally random (sometimes 10x within 5 minutes, sometimes it runs OK for 2-3 hours before the problem strikes again) I now supect something wrong with the cable. I now rfeplaced the original cable with another SATA to USB3 adapter, and am now running since about 4 hours without any disconnect. Fingers crossed this will continue this way!
Apart from a flaky cable, this also could be a compability problem with the bridge controller in the cable itself. The cable that came with my Fusion Flex has a ASMedia one while the new adapter I tried apparently has a JMicron one.
Just FYI! And maybe we should report this to Sonnet as well since it seems not to be an isolated case.