Sure
I'm using the following setup:
MESS 0131
Cmd Line: mess.exe -nonu -now a5200 -skip_gameinfo -cart "[rompath]\[name].[romext]"
zipped roms containing .a52 carts
The bios for the atari 5200 is in mess0131\bios\a5200\5200.rom and is 2k in size.
I think it has something to do with your bios, try another version?