When I bought my 05 WR the PO told me he had replaced the piston and barrel due damage that occured due to "it running lean when it ran-out of fuel at high speed" (he had been using it on the road). Soon after buying it I blew the head gasket when at full noise going up a long steep hill. I pulled it apart inspected everything (all OK) and put it back together with new gaskets carefully following the torquing procedure in the manual.. One thing I noticed when I pulled it apart was the front right head stud was barely finger tight - so I suspected the PO hadn't torqued the head properly. After another about 20 hours the head gasket blew again. This time a put a spanner on right front bolt and was amazed to get about 1/2 turn on it. That seemed to seal it up - but after 20 minutes it blew again - and yep, I got another 1/2 turn on the front right stud. I did this a total of 4 times - thats around 2 turns! On pulling it down it is clear that stud has stretched.

The studs are shaped/wasted, which leads me to suspect they are designed to yield on tightening. If so, it means they are designed as a one-time use.

The interesting thing is that the manual does not advise using new head bolts - unilke a lot of other things which it clearly points out should be replaced, and I (and the mechanics at local Yamaha shops I have talked to) have never heard of this happening before.

I believe the primary function of the shaped/wasted studs are for lightness. I've never heard of anyone needing to replace them before, that is, except in your case. Are you using stock oem gaskets or aftermarket? Big Bore kit? High compression piston? Any or all of these will put more stress on the components. Maniac

Along with what Manic said. Something is yielding and relieving the clamping force. Could be gaskets (use only factory gaskets if you can), The bolts themselves are torque to yield bolts, that means you torque them, then add 180 degrees of rotation to stretch them. These types of bolts are typically one use only in my experience (automotive). Perhaps yours are shot, bad temper (from the prior meltdown) or re-used too many times. You confirmed you used the proceedure in the manual, did you put the moly grease on the threads and the washers?. The washers are there and are correct? Are the threads OK. Have you checked your head and cylinder deck for flatness?
I would get the head and deck checked for flatness, check the threads in the cases, buy new OEM gaskets, bolts and washers, a tube of moly grease. Only about 10% of torque is transfered into clamping force. The rest is absorbed in head and thread friction, which is why the moly grease is required.