I'm trying to figure out what could be causing the problem. In theory, if the shocks are the exact same length and the swing arm is straight, the second bolt should slide in easier than the first because it should already be lined up perfectly.
Is the chain guard interfering with the installation? I know many non-stock shocks cause problems with the chain guard because the spring sits much lower on them than on the stock shocks, so the narrow section at the bottom is much shorter.
Does the bolt easily thread into the bottom of the shock when it isn't on the bike? If not, maybe it's the threads of the bolt hole that's the problem.