I setup a test which base64'd EICAR and wrapped it in XML.
The virus signature was not detected. If the file contains just the base64 encoded signature then the virus is detected.
I'm not sure if this means that the virus scanner isn't able to understand XML if it is because the EICAR virus signature is only activated when the file contain exactly 68 or 70 bytes. Once the xml tags wrap the EICAR it is no longer detected.
So not sure if the test means all viruses wrapped in XML tag will no longer be detected or just this virus signature.
If I extracted the base64 data and save that into a file then the virus scanner detects the virus. Naturally it would be better if the virus scanner recognised the base64 in the XML and did the checking appropriately.
Try (if you havn't already) the /MIME switch.