Do you have any idea why clamav refuses it? The funny thing is it doesn't happen all the time. Most of the time the update completes succesfully, so I figured it can't be the clamav database being corrupt.
I have no idea. Maybe you can try to turn on logging for Clamav. The complete clamav installation that ISPConfig uses is in /home/admispconfig/ispconfig/tools/clamav
There is one workaround that you might try.
1) Install clamd (the daemon version) from your linux distribution.
2) Reconfigure the ISPConfig clamassassin script in /home/admispconfig/ispconfig/tools/clamasassin to use the clamd daemon instaed of the clamav binary from ISPConfig.