I also have this problem. Memory limit on my server is set to 276M (so more than enough i presume). No errors on the last 300 err list. Feedback is appreciated.
One small note - I have the premium account and in progress status is shown for these:
Feb 20 07:45:01]
Comparing core WordPress files against originals in repository
[Feb 20 07:45:01]
Comparing open source themes against WordPress.org originals
[Feb 20 07:45:01]
Comparing plugins against WordPress.org originals
[Feb 20 07:45:01]
Scanning for known malware files