I forgot to attach the two bumpers before reassembling my MBP the first time I baked the logic board, so I saved them (for the next time). I needed to do another baking, so I reinstalled them after I was done. I did not have trouble reinstalling the screws as you describe - so maybe some part of the melted bumpers is obscuring the holes?
Thank you ifixit! I used this guide to remove and replace my logic board in my early 2008 MBP. I am among the successful (so far) ones who managed to reflow the gpu solder via the oven method. I purchased a few items from you to do the job. I had nothing to lose, so I went for it - and a detailed step by step guide no doubt was key to my success. The Arctic thermal paste was important to the reassembly as was removing all the dust clogging fans and heatsinks. My machine, which has been sitting collecting dust since last summer is humming quietly - I was able to upgrade to Yosemite on this old workhorse and testing it now. Woo hoo!