There may be two answers.
1. Some registry entries may be re-created by a background running program or a service.
2. There may be some permission restrictions set that do not allow to modify registry entries.
1. First, ensure that you can delete/modify problem entries:
do a registry scan with Registry Healer, select the problem registry entry in the list of found errors and double-click to open RegEdit at the entry. Then do a fix with Registry Healer, switch to RegEdit and press F5 to refresh RegEdit window. Does the entry disappear?
If it DOES and you still see the same registry key on next boot, then it is re-created by some program. Either find that program or simply add the key into Registry Healer excluded list.
If it DOES NOT, then your account probably has no permission to modify that registry key. Try to delete or modify - what Registry Healer suggests - manually from RegEdit. Is RegEdit able to delete the entry?
2. If you are unable to manually delete the problem registry entry from RegEdit as described above, then it probably has access restrictions.
Permissions can be viewed and managed using RegEdit.exe. To view/modify access permissions user can open the question registry key in RegEdit.exe, click "Edit" from top menu, then "Permissions" menu item.