When I try to upload a file using the cPanel File Manager (any file) I get the following error:

Virus Detected; File not Uploaded! (Can't parse configuration file.)

I guess the uploadscript tries to scan the file for a virus, but a configfile tor the virusscanner is corrupt/missing.
Where can I find this file, or disable virusscanning during file-uploads.

remove your clamconverter in the cpanel modules in WHM

I found the answer on the cPanel.net forums:

Have a look at your clamav.conf in /etc

Look for this line at the top:
# Comment or remove the line below.
Example

As the conf says comment out the line, so it looks like this:
# Comment or remove the line below.
#Example