certainly not a hardware issue.
Why am I so sure? I have been playing with this box for the last 3 weeks and have set up no less then 10 SW RAIDs through various OS's (opensolaris, ubuntu, gentoo, redhat). I have not seen this issue until I started using the Open-E software.

To note the adaptec controller has the latest firmware already.

The only issue I can see is that perhaps the 2 controllers are having a hard time talking to each other, the on board SATA controller and the Adaptec Controller. While this would likely be a software issue I've not read anything on this site or in the manuals to state that this should be a problem.