When you say word documents do you mean microsoft word documents? And when you say "native email server" I suppose you mean native email client (modest). Anyway I tried sending a MS word doc and as expected it comes out exactly the same on the receiving end (checked using md5sum). Unless there is an obscure bug in modest there is no reason at all why it would mess with it at all.

If it's not user error (on your part ) then one possible cause is that the email servers (either or both the sending and receiving) is doing content filtering (antivirus, antispam etc) and has somehow altered your attachment. However if they did alter anything they usually include a note saying so and maybe why.

If it's an obscure bug with modest you could try zipping the word doc and see if that helps.