I've been having this same issue for a while on my iPad2. After scanning this post, I decided to start removing items from the misbehaving folder. No change, until I got to Camera Prime (iPhone app). This app does not have any control panel settings for badges, but does have an internal option (by the way, the folder showed the badge number -3). Upon removing the offending app (Camera Prime), the count immediately corrected.
Attempt 1) I opened the app, turned off the badge count (no badge showing on the app by the way), and then put the app back into that folder. Count on the folder dropped by ONE only.
Attempt 2) Deleted the app, reinstalled from the cloud, put it back in the folder. Count drops by ONE. Tried deleting through the control panel (deletes data as well), then reinstalled. No change.
Test1 - Moved the app to a different folder (with a badge count), count reduced by ONE.
Test2 - Moved the app to a different folder with NO badge count. No change.
So I've reduced the effect of the count, but this app (Camera Prime) seems to have a defect that is (perhaps) a default count of -1.
Have not tried resetting the iPad since going through this. Maybe later.
Good luck.
