"
After updating to the latest virus defs (20140612.006 I think), it continues to scan around 5,300 files"
You are still not getting it, Symantec will change this when necessary, could be tomorrow could be in 10 days or more.
It doesn't mean that the next Virus defs will change it.
Since 1 day or 2, on 3 systems, 2 W7 x64 and 1 XP SP3, I have also this behavior, about 5000 files scanned intstead of 9000+ files.
Stop worrying...
Hope this helps,