I don't have an automated setup, I just click on the exe to open Filebot, so I don't know how it possibly could be activated multiple times.....
Well, logs are logs, and I can't tell you what to do since it's definitely a client-side problem. You could check your logs, and see if you get the corresponding "Activate License" entires.
Reasons the system might have flagged your license:
1. Activated from 5+ countries in a short period of time (normal would be 1-2)
2. Activated many times in a short period of time (normal would be 1-5 times per month)

Note that fixing (2.) will also alleviate (1.) as less activations means less activations from different countries.
The first post of this thread should give you the general idea as what's going on, application state is reset between runs, leading to premature "Activate License" requests. This could be for any number of reasons. Some guy had a 3rd party tool that periodically deleted all application data files. Could be anything though. Keeping logs and checking them would be a good first step to figure it out.

Some users may have genuine use cases, that are unfortunately virtual indistinguishable for abuse, in which case I'm happy to just offer a refund.