I have a problem that did not exist at a previous system restore point. I want to find out the difference. Is there a built-in or third party program that can list the differences?
I don't know of a tool that can compare restore points.
However, as explained more in detail in Dump Registry to text files for tracking, you can very simply restore the two and then export the entire registry as two (huge) text files. You can then use a text compare utility to find out the differences.
If you choose this solution, don't forget to create a current system restore point that you can return to.
Restore points are very protected by the system so viruses will not be able to miss with them that's why it is somewhat hard to compare restore points.
Ironically, a virus-infected system will include viruses in the restore point :)