We have similar problems with a small selection of machines (we currently have approx 1000 machines, and this problem occurrs on around 50).
When it does occur however it is quite pronounced - IE scans can take 10+ hours (I have one client machine where the scan takes over 24 hours) and the machines are quite badly affected during the scan, CPU usage on RTVSCAN is quite high, but more annoyingly, access to all other functionality on the machine is dog slow.
SEP is turned down for best application performance, and all the affected clients are on 11.0.4014 - it affects a variety of OS XP sp2, sp3 and Vista RTM and Sp1, and the spec of the machine doesn't make a massive difference.
There are some very definite themes running through all the machines affected though - most have a combination of:
Disk full or close to full
Lots (many many thousand) of small files
Lots of compressed files / big compressed files (often with many files within or several levels of compression)
Significantly fragmented drives
Drive intensive applications
Sort out most of the above, and the scans become normal again - problem is, I often can't sort out the above due to the nature of the jobs of the people using the machines (developers).
My advice to the OP is to try to optimise the scanned machine as best as possible and then see if you still get issues (use a test machine first).
Do things like remove .zip .cab files where possible, clear down the $backup stuff$ in Windows/Winnt directories - don't forget the Software Distribution folder - this almost always has a build up of files in it.
My request to Symantec is - Please make the scan throttling work - I don't really care if scans take a long time, as long as the machine is usable whilst it is doing. (please also allow scans to start where they left off if they get interrupted)
Nick