OK, so I'm getting sick of being restricted from using new features presented by Google (the most recent being the check-in feature on Latitude), so I'm seriously considering moving back to an @gmail.com account.
Does anybody know if there is there a way for me to do this and not lose all the apps etc that I've purchased with my custom domain?
It's a bit silly but you can create a Google account using your Google Apps email address and have both on the phone at the same time, and use the Google account for Latitude. See here. Make sure your sync settings on the phone are set to only use the Google Apps account, because they have separate calendars etc.
I don't know why they have such problems using Apps accounts, there must be some extreme awfulness going on behind the scenes.