Hi ps4isthefuture.
I never used Nebula and haven't used WinKawaks in yonks so I can really only speak for Mame.
I use LaunchBox for my Mame games which include many NeoGeo and CPS1/2 titles and I have no problems.
The only Mame issue I've had with LaunchBox was with the so-called romless games, where the game's name is actually the folder containing the CHD file.
Mame runs these ok, but LaunchBox returns an error if you try to launch a folder.
I use the dummy zip rom fix to get LaunchBox to launch these romless games.
The following might be your problem with trying to run your NeoGeo and CPS1/2 games under Mame.
I've noticed that there can be differences between some of these NeoGeo/CPS1/CPS2 "official" roms and their Mame equivalents,
For example Progear (USA 010117) "official" CPS/2 rom has 2 extra objects that are missing from the Progear (USA 010117) Mame rom.
Mame will run the "official" CPS/2 version as it contains everything Mame needs for this game.
However, the NeoGeo "official" of Metal Slug 3 (NGM-2560) will not run on Mame as it's internals differ from the Mame Metal Slug 3 (NGM-2560) version.
If you want to use Mame for NeoGeo and CPS1/2 gaming you should use Mame versions of the roms.
Sorry for not being of more help to you.
Best of luck with Kawaks & Nebula issues.