Interesting that you swapped out the extractor. I have a 700 in .308 and every once in a while have a job forcing home the bolt.
Remington bolts have a floating extractor and sometimes (not often), they move off centre meaning that when pushing the bolt home, the extracting lug cant grip the bullet base correctly.

See below

http://www.picparc.co.uk/rem-700-no-fit-brass/