Depends on what build is on your nook color. You might want to check out the following site for info on modding your nook color. Portal:NookColor - nookDevs
I can tell you what I did to fix those issues on my NC with CM7 on the eMMC (and hope they work for you). If you have ROM Manager installed try using the Fix Permissions option under the Utilities section - if you do this make sure you power off afterwards by holding the power button, not using the software buttons. If that doesn't work you can try Titanium backup from the app store, make sure you choose "Backup all use apps + system data" from the batch file options. Hope this helps!