This topic should definitely be under newcomer's board.
Second of all, there is no difference between the IPS patchers. The patch is important, not the patcher. The IPS contains a list of all changes: the location in a rom, as well as the new code, so how can one patcher be different from others, if the changes are recorded in the patch itself (any IPS patcher just "does" what the IPS file is saying).
Lunar IPS is not outdated. The only difference between the IPS patchers could be, that some auto-ignore the header, which is what IPSwin did.
The rom, which is not working, is a result of false patching= patching to a wrong original rom (in your case you patched to headered rom, instead of non-headered). And the Lunar IPS, and IPS in general is dumb enough, not to include the crc id of the hack and thus can not see the difference between the correctly patched and bugged rom (it says patching successful in any case).
The IPS is also a linear patching format (can not handle any shifted data. So if someone uses the headered rom for base and non headered for modified one by accident, it would think the files are completely different, which is again dumb).
To anyone, who is making patches: make UPS or xdelta, not IPS.
The extensive info on the original rom and header info on the site under ROM info is obviously not enough to prevent false patching.
Regarding the removal of the header: Tush program for rookies, but a true hacker will of course use the hex editor.