Having two roms with the same name, even if they are in different folders, is going to be a issue. Here's how I think Attract-Mode (AM) can solve it for you. Remove the second rom folder from you existing emulator in AM and create a new emulator in AM with the same settings except for the other rom folder. This will cause each AM emulator to only use one rom path. Once both of these are emulator setups are work properly you can combine the romlists in AM to get the romlist you want.
1. Change your existing advmame emulator configuration in AM (I'll assume it called advmame in my example) to only use one rom folder
executable C:\attract\sistems\capcom\advmame.exe
args -m "[romfilename]"
rompath C:\attract\sistems\capcom\roms
romext .zip
system arcade
2. Create a new emulator in AM and call it advmame2 (only for my example, you can use whatever you want but need to adjust accordingly) with this configuration use the other rom folder
executable C:\attract\sistems\capcom\advmame.exe
args -m "[romfilename]"
rompath C:\attract\sistems\capcom\roms2
romext .zip
system arcade
3. Backup your existing romlists that use advmame... just in case things don't work the way you want so you can revert back to what you have now.
4. Regenerate romlists for advmame and advmame2 emulators in AM
5. Create a combined romlist of advmame and advmame2. This might take a while to build if you have a lot roms.
Configure-->Emulators-->Generate Collection/Rom List-->Set your advmame and advmame2 game emulators to “Yes†and then click “Generate Collection/Rom List†and enter the name “advmame_all†(just for my example, again you can choose any name here)
6. Hide your two split romlist displays from AM GUI
Configure-->Displays-->advmame-->Show in Cycle = no
Configure-->Displays-->advmame-->Show in Menu = no
Configure-->Displays-->advmame2-->Show in Cycle = no
Configure-->Displays-->advmame2-->Show in Menu = no
You should now have a new display called advmame_all that has both versions of the same roms in different folders that all work correctly in AM.
You might want to look at this thread on similar solutions on how to get exactly what you need from AM
http://forum.attractmode.org/index.php?topic=1165.msg8455#msg8455.