Hi virtualcop, welcome to the forums.
avast! only appends text to emails e.g.
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avast! Antivirus: Inbound message clean.
Virus Database (VPS): 0439-0, 20/09/2004
It doesn't delete text, if an attachment is found to be infected, yes it will warn you and you make the decision what to do. avast! doesn't act independantly (unless you set it up to do so).
Is it possible that the email was empty to start with (what were you using to ckeck it on the GMX server)? Did it come from an expected source? What was the attachment? What version of avast are you using?
There are others in this chain, the senders ISP could be running an anti-virus/spam program that could have an effect. Your ISP could also be doing the same. Are you running some form of anti-spam software?
As you can see there are a lot of questions, we need mor information. You say sometimes this happens, is it always for emails with attachments, from the same source, etc. etc.