Initially AROS ROMs were not working with "old" UAE/E-UAE ports while they worked with WinUAE. The reason was that AROS ROM required serial port to be working in the emulator. Maybe this has change since then, but I would check if your emulator has that working.
Here is a patch that added the support to Janus-UAE:
http://sourceforge.net/p/janus-uae/code/640/