Don't mean to hijack this thread but I have a very similar issue as the OP (donpachi as well, vert on a horizontal).
If I run: mame donpachi, I can get the game to run but it looks crazy ugly as I'm assuming it is virtualizing and stretching the screen to fit my monitor.
If I run: mame donpachi -cleanstretch, I get like the OP and get a black screen, but i can put coins in and hear the sound.
If I run: mame donpachi -noswitchres -triplebuffer -mt, It runs clear and clean at 100%. with black bars on the side as I am playing vert on a horizontal.
Using hyperspin as my frontend, I have setup another wheel for my vert shmups (with the different command line changes) but would rather have all my games under the mame wheel. It feels like the magic resolutions are scaling when it doesn't need to? Am I wrong about this?
Settings:
groovy mame 146
ati4800 with soft15khz for 15khz and 24khz res installed
Nanao ms9-29 with proper mon settings in the .ini (taken from this forum)
I've attached my logs.