You might also try disbaling the rescan of the file cache on def update, which is separate from the options already mentioned above.
http://www.symantec.com/docs/HOWTO27136
This is found in the Virus and protection policy, under Auto-Protect -> Advanced -> File Cache -> Untick the option to "rescan cache when new defintiions arrive".
Note: this rescanning of the cache is only a performance setting, and does not affect security.
Essentially, all the file cache does is keep track of files SEP believes to be clean. The "rescan on new definitions" is there just to front-load the effort of making sure these files previously thought to be clean, are still clean. Without the rescan, SEP just waits until the file is accessed again to scan it with Auto-Protect.