The only other issue I've run into is lack of RTC being a bit more trouble than I'd anticipated for some things. None of the stuff I'm building directly has any hard dependencies on linear time, because it wouldn't be much of a reliable or deterministic distributed system if it did ;-), but some underlying facilities that I depend on don't take very kindly to having their clocks reverted back in time on a regular basis.
Those minor foibles aside... these are exceptional SBC's and very, very competitively priced. I'd probably donate a kidney for a proper SATA port on them though. :-)