Hi,
You're probably right and some flag is not getting cleared.
Can you try to perform full scan - apps AND external storage? That should clear the flags for good.
Also you have to scan all external storages, if you've changed it to some directory. Don't just select STORAGE #1 by long pressing on it and tapping SELECT on the top, but tap Select on the bottom instead. You should see "all storages" on the Virus Scanner settings screen after that.
Thanks,
Ondra