I'm running WM6.5.1 fairly stably on my Apache (Can't get my flash going in Opera tho!).
AFAIK, (at least what I learned from JustPCTech at PPC Kitchen) your extROM should not have been touched during the flash to the new ROM. You can poke around in this form for information on
unlocking the extROM and see if that sheds any light on your question. I haven't messed with it personally, but I can see how being able to use it might be helpful. Last I looked, they mentioned not being able to 'lock' the extROM after unlocking it - which is where I stopped. Good luck!