@Cliff - I tried what you said and got 404's on any of the pages that were being rewritten to .html pages, so it does seem that the rewrites are being handled. Thanks for trying... I think that you might be onto something with the processing order. I'll have to take a look into it in more depth. Frustratingly, I restored my backup vhosts .conf file, and now it doesn't seem to want to load any objects in the /arcade/gamedata folder, which is preventing some of the games from loading.
@Edho - What other information do you need? I didn't want to put too much for the sake of brevity, but I can post whatever you think might help.