Is one of them 32 bit and one 64? Are you having some issues because they don't match?
One thing that I can think of that may cause the versions to be different is if you installed them at different times and chose to update the install files. There are some updates that only get instailled when you update the install files, not when you install rollup 1.
Probably the best way to get them to match exactly is to uninstall each (leaving the databases in place) and install pointing at the existing environments, choosing to update the install files, then install rollup 1 (and the new rollup 2 if it solves any issues that you are having).
BTW--with rollup 1 installed it will always tell you that an organization that you are importing has a different version than the base organization when you import an organization via the deployment manager. I have found this even if I import a copy of a database from the same environment and try to set up another tennant in that same environment. This doesn't seem to cause any problems.
