Thank you for the replies. I still don't have a window.am, even after having changed to window mode to various settings and having restarted, so I'm unable to delete it.
So for now I will edit out the window mode parameter from the attract.cfg as per keilmillerjr's recommendations and will try again this afternoon when I get back to the crt, I'll report back the results after doing so.
It's probably not the emulator that's at fault here because the issue I have begins the moment I open attract Mode itself while on the crt. I don't see anything other than a black fuzzy image with horizontal lines moving at fast speed up or down. At this point I need to disconnect the vga from the crt to go back to the lcd to get a proper image and then all works fine, of course the moment I quit attract mode I end up on a black screen on the lcd and have to go back to the crt to see windows properly in 640x480i 15khz.
I think this might have something to do with the fact that I configured Attract Mode on the lcd before moving to the crt. So am I correct in assuming that thre is no frequency setting so technically the image is still being sent in 15khz but the lcd digitally processes it to work despite the 31khz requirement there?
EDIT: By the way do different themes have different compatible resolutions? I'm using Game Station and wondering whether or not it is compatible with 640x480.