"Not Responding" does not always, or even most of the time, mean that the program is failing.
It simply means the program is too busy to respond to the OS asking what's going on. Windows periodically asks a program to respond to it to make sure it's still functioning properly. If a program is particularly busy it may not be able to respond to Windows' query. It happens. It usually doesn't mean anything.
Your Inbox Repair Tool is probably very busy at the moment repairing your PST file. In my experience, based on the size of the PST and the nature of the issues, this repair process can take hours.
So be patient.
It's possible the issues may be too much for the tool as alancc notes, but 5 minutes is not nearly enough time to know that.