Finally, after a good 2 weeks I've got my rig setup and stable for once. If you have this mobo, it is very finicky with settings after you put the cards on 16x to 1x risers. Had no problems with my 2 290x's on the mobo directly, but after going to an open rig have had nothing but issues. This mobo isn't the best at telling you what's wrong (not to mention there is no onboard power switch and if, like me, you've been using a tiny pin connector to turn it on and reset it, I feel for ya) and you've probably been pulling your hair out trying to get it to recognize cards and stay up for more than 45 minutes in cgminer with "stable" settings in your conf.
After doing some digging, it turns out that with the R9 series cards you need to set the PCI slots in BIOS to "Gen 2". DO NOT leave it on "Auto", that won't work. Props (and tips for the help) for discovering the solution goes to
Vyker over at overclockers.net.
I also am using the modded and "fixed" for R9 series cards cgminer on Ubuntu 13.10 from
OhmPie; if you haven't come across it yet, using the --gpu setting in cgminer for the R9 series cards can cause some to crash, have blank screens, freeze, etc. He gives a pretty good breakdown of why cgminer has issues with the new R9 cards and what he did to fix them.
However, YMMV with the settings you're familiar with on the cgminer 3.7.2 build as OhmPie uses 3.7.0 cgminer. What I can say is since I moved to the OhmPie cgminer and Gen 2 on the PCI slots is that I've been very, very stable over the past 24 hours (for once).
I'm also pretty sure this is the last MSI mobo I buy for mining ...