The best way to figure out a problem registry entry that should not be modified is to correct all invalid registry keys found by Registry Healer, then re-install problem software, be sure that it works and scan the registry with Registry Healer again. More likely, Registry Healer will find some new invalid registry entries and some of them will belong to a problem software.
From this moment you can correct every single invalid entry (with creating separate backup files) and test your software after every single correction. If a problem program doesn't work after last correction then that registry entry should not be modified. Restore it from the most recently created backup .reg file. Be sure that a problem program works fine again and add that registry key into exclusion list.
In this way you will able to find one or more registry entries that should not be modified. Add that entries into excluded list using right-click pop-up menu over the selected entry.
If you have no time to complete this deep test, you can simply add into exclusion lists all of the new registry entries found after re-installing your problem software.
If you have no installation file of the problem software or the above instructions do not help, you can try the following.
If you've cleaned empty entries then restore your latest backup .reg file of empty entries. For example file "empty_2001_10_21.reg". Then run the program. If it fails then restore a previous backup file, for example "empty_2001_10_20.reg". Run the program. If it fails again then restore all backup files one by one and keep trying to run the program after each backup file to figure out the problem.
If you haven't corrected empty entries then restore your "Invalid Paths" backup .reg files in the same way as described above.
1. Restore your most recent backup .reg file.
2. Check if the problem still exists.
3. If the problem exists then restore your next .reg file created before the most recent one. Restore .reg backup files one-by-one in backward order (from the most recent file to the most old). Test for the problem between restoring the backups. Do these steps until you find that the problem disappeared.
4. If the problem has gone this means that the latest restored .reg file contains a modified registry key that caused the problem. Please send that backup file to email@example.com. If the problem persists then you can restore the most recent full registry backup file. If that doesn't help then the problem is coming not from damaged registry.
5. Scan the registry with the program.
6. Select for correction only first 10-20 found invalid entries and correct them.
7. Reboot the computer and check if there is no problem.
8. If computer works OK then scan the registry and correct next 10-20 invalid entries. Do the steps 5-8 until you find that the problem re-appeared.
9. If the problem re-appeared then the most recent .reg backup file contains the problem registry key within 10-20 modified entries.
10. Restore that backup file, scan the registry and correct invalid entries one-by-one with checking your system functionality between corrections.
Following this procedure you will figure out a problem registry key that should not be modified. Add that key into the exclusion list - right mouse click on the selected key in the list to pop-up menu and click the "Add the Entry into the Exclusion List" menu item.
After you have restored your program functionality please scan the registry and try to find within found invalid entries a registry key that corresponds to the problem program. Usually it looks like "HKEY_LOCAL_MACHINE\Software\your_problem_program_name\....". Unpick the all found entries, pick this only entry and made changes to the registry (with creating an individual backup file like "C:\Program Files\Regheal\trouble_1.reg"). Then run your program and check if it functions properly. If it runs OK then restore that corrected entry and try to find another problem entry using the previous method. When you find the problem entry (after correcting it your favorite program doesn't work), add the entry to the exclude list.
After that run the registry scan, make registry changes and be sure that your program works OK (found problem entry will be excluded from the registry scanning).
This problem finding algorithm is useful for all faults that may appear after healing the registry using Registry Healer.
Please also send your found excluded registry entries with detailed description of the problem - what applications do not start, do not work properly, etc. to firstname.lastname@example.org. This will help you to avoid the same problem with future versions of the program.
Running Registry Healer once a week in the future will decrease the number of invalid registry entries, and correction will not be a problem.