There are three possibilities:
- Online: Monitor the changes online
- Offline 1: Use a tool that collects all information about the available files into a log file (e.g. a checksum file) at the beginning of the period and again at the end. Afterwards the logfiles can be compared to see what changes
- As NTFS supports snapshots (aka Volume Shadow Copies) you could manually create a shadow copy at the beguinning of the period and and the end compare both versions
The one-in-all tool for online monitoring is Sysinternals Proces Monitor (free) - however you you only want to see what changes configuration can be a bit difficult and I am not sure how stable it is for long term usage.
Offline Monitoring by "Checksum file"
Even if the name shows that it's primary focus is monitoring the Registry RegShot (GPL) also includes file comparison. There are other alternatives like SpyMe Tools and SystemSherlock Lite.
Offline Monitoring by Shadow Volume Copy
I don't know of any tool that would allow something like this. May be a talented programmer reads this and takes it as an idea for his next project?