What model of the console are you using? I only have a PAL TG16 myself, so that's the only kind I can test with.
I really have zero documentation about how the cart works. The way I made the updated menu was by manually disassembling the original menu with the help of an emulator, and then adding my own code for listing multiple games and loading some additional graphics. But the actual loading should be exactly the same, so I'm assuming you have the same problems with the original menu(?)
I'm sure the problem is not your menu. it happens with the official menu when using the OSX loader software too: http://www.neoflash.com/forum/index.php/topic,5941.0.html
My consoles are a US Turbo Duo and a PC-Engine LT.
I will try your menu using the official writer and see what happens. I'm sure it will work. I like that it shows more than one game at a time, plus it does not cause the same sort of "burn in" that the stark blue background and white letters cause. I find I can see a ghost image of the official menu on my LT screen and it probably does the same on an LCD or PLasma TVs too. yours has muted colors and is much more subtle.