I posted this to a topic in the 29er forums. Basically I'm having a creak too on my Pro29.
Mine, a 2010 Pro29 w/ the newest sliders is creaking. I've checked and doubled checked and then triple checked for cracks and can't find anything. I've run it SS and 1x9. I've replaced/changed out EVERY part on the bike at least once. I don't know what's causing my creak but it's beyond annoying and it seems that it could very well be the frame. It only seems to come out when I'm on the trails putting a load on the bike and once it starts it doesn't stop. Wheels, skewers, BB's, cranks, seat posts, seats, chain bolts, pedals, cleats, shoes, chain, casette, stem/bars, fork, headset, seat clamp, brake mounts, SS or geared, a 1/2 tube of Phil Wood grease AND the thing still creaks! I'm out of options and I can't/couldn't recreate the creak with the parts on my other bike. The Pro29 makes an awesome bike but I'm not sure how much longer i"m going to deal with this creak. Sadly, I have Helix road bike and have absolutely NO problems with it.
My problem is just like what the OP is experiencing. It's hard to reproduce the creak unless I get on the trails. One thing I did today (the bike is setup as SS right now) was reverse the skewer. I put the locking side of the skewer on the driveline side. I haven't had a chance to test it but strangely enough, the first time ever, my rotor/disc didn't bind up and it's the free'est my rear wheel has spun. Not sure if it'll stop the creaking but at this point I'm willing to try anything.