For your second question, no. Every time the exe changes, it is a new program to the firewall. Allowing you to specify a folder as being safe would defeat the point of having the firewall monitor. If malicious software were to infect your exe and access the network or Internet, the changed signature would not be caught by the firewall.
If you firewall keeps turning off on its own and requires the use of the repair tool to get it running again, I recommend you contact support to determine the cause of this problem, likely to be a conflicting program or service on your PC.
-steve