I have played several PBEM games of BoA2 without problems, so It should work.
- be sure both have updated the game to the same patch.
- Don't use the turn compresion or password options. They use to give problems
- Use Dropbox or a similar cloud storage system to send turns. It's much easier and faster than email.
Hope you solve your problems! BoA2 is awesome on PBEM!