To reproduce the jv16pt vs StartRight incompatabilities you infer, I installed StartRight 1.3.1.1521 on my desktop PC.
1. It moved the HKLM Run items to its own key structure in HKLM\Soft\JackassArswareOrg\StartRight.
2. It did not touch the HKCU Run items (there is one in my registry).
3. There were no problems during a restart.
4. jv16pt Registry Cleaner showed no errors related to StartRight.
5. jv16pt Startup Manager showed only two StartRight items and the one HKCU Run item (expected).
6. There were no problems during a second restart.
7. jv16pt Registry Cleaner again showed no errors related to StartRight.
Conclusion: There were no jv16pt vs StartRight incompatabilities in the above scenario.