We have noticed the same on several SME (6 and 7) servers over the last few weeks. On SME6 where the ClamAV installation is a contrib, the freshclam updates are scheduled via cron. There it looked like a former freshclam job never finished and blocked any further freshclam jobs.
In that scenario, we had to kill the 'hanging' freshclam, ran a freshclam manually and after that, the regular (cron) jobs started working again.
Under SME7, we restarted the freshclam service (/etc/rc7.d/S80freshclam restart) to get things working again.
I believe that the problems come from the remote server end and not from the SMEserver installations.
Judging on the ClamAV 0.88.6 changelog ("freshclam: apply timeout patch "), I hope that this version will help (fix?) with that issue.
Michael