I don't have an HD2 so I have no idea. It could be the ROM you are using is causing you trouble? I would suggest you try a few things:
1. If you have recovery installed then backup all of your apps, text messages, contacts, etc. and then boot up into MAGLDR then recovery. If you wipe data then it will reset the phone as if it were the first time you ever installed the ROM (so it will have no apps installed, go through the first time setup for your accounts, and so on). While you're at it, go ahead and wipe cache, then go to advanced > wipe dalvik cache.
2. If you don't have recovery (or even if you do) you could flash the same ROM or a different ROM on the phone. Again, backup anything important to you and then just boot into MAGLDR, pick the USB flasher mode, and run the .exe for whatever ROM you desire. It should overwrite everything in data, cache, and dalvik with the new ROM info.
Not really sure what else to recommend besides this. It's a rather unfortunate answer I know.
MyBackupRoot is a pretty good app that can backup most things for you. Whenever I install new ROMs I generally just pull the apk files I want with adb and use SMS backup and restore to save my text messages (all of my contacts are already saved in google). Once the phone is running the new ROM I can just use adb install to put all of the apps back on there (or download them again).