Ah, I see. Well, you are right... the thing is that the whole Move/Rename action is rather questionable. The preferable action is Move to Chest - which protects the file from being detected subsequently.
Regarding the solutions:
1. Adding *.vir to the list of exclusions is certainly possible, but I wouldn't do that by default. The list of exclusions is not exactly optimized for bigger list (i.e. it's not recommended to put tens of different masks there - it may slow down the scanner), so the smaller the number of default exclusions, the better (especially when the Move/Rename action is used only rarely).
2. Sounds interesting... I'll probably add this check; I hope it won't cause any problems...