The requirement for both OOBS to be 100% in synch is in the manual. It is to prevent cheating (e.g someone editng an OOB so (say) his M1 cost 20 points).
It may be possible to recover your game by doing getting player 1 to send you his OOBS. (Player 1 sets up the game, and therefore the checksum is taken from his OOBS, and not player 2.)
However - you really should establish between yourselves who has the official and most recent oob set. If his are older, or are hacked oobs, then you will want to restore your more recent (or non hacked) oobs at some point.
You can always use the "manage OOB sets" function of the Game Options programme to handle this. Make a folder for these oobs as a custom set and then load them as necessary, you have a backup of your originals in the default OOB set.
The version number is shown at the foot of the game's main page. look for "WinSPMBT vXX.XYY" where XX.X will be the numeric version number and YY is DL or CD for downloaded or CD version (and is irrelevant to PBEM unless you want to use the CD extra facilities, such as tournament play, when both of you will need the CD version).
Get your friend to update to 2.51, and then you should be in business.