Creating IPS exceptions for Signature 1000-1003 is not recommended, as these are the HIPS self-protection signatures. These signature prevent users/applications from gaining access to HIPS files/registry/process activity. Instead, find a way to prevent the 3rd party application from triggering the signature (through its own configuration; exclusions, etc.)
Creating exceptions for Sig 1000-1003 can compromise the HIPS product functionality (i.e., 3rd party could gain access to modify the HIPS process in memory, or files, or registry, etc.).