I don't think the original poster's problem is data corruption: I think it's a bug. I can easily reproduce the problem.
I created a New test Quicken file. I added a checking account and a savings account.
I created a new Custom Category Group named "Savings". I assigned the transfer TO my savings account to that new "Savings" Custom Category Group.
I selected the TO Savings transfer category in an otherwise empty budget. My budget showed the "Savings" Custom Category Group twice - just like the original poster's display.
See attached.
Qbo said: Same problem here - Custom Category Group creating duplicate Budget Group - solutions please?