We have just upgraded from Avast 4.8 Pro to Business Protection and have just found the same issue - Outlook 2007 and Exchange Server 2010. Again not all emails are stripped. Thankfully it appears that you can check sent items folder so see what messages have had their message bodies deleted.
I also had this issue with Avast 4.8 about 18 months ago and support told me that Outlook 2007 and Exchange Server 2010 was not supported with Avast 4.8. Now we have moved on a version (or two), I had expected this to be working. Thankfully I had only deployed this on 3 test machines.
In this case, my solution was to disable AVAST outgoing message scanning in the 4.8 control panel which was not a huge hit, but we are now deploying automatically and I have not spend enough time with Business Protection to find if there is an equivalent setting that I can disable and, more importantly, deploy remotely.
The work around for now seems to be to manually disable AVAST plugin in Outlook 2007 but this is a per user option and I cannot continue to rollout Avast on any other machine until this is resolved. I will see if I can reopen my old case.