Hi Nina,
After having the same problem and doing all the recommended actions in OKEON KSH3 eg ambiguity, test, check, master data etc I could not fix.
I found SAP NOTE 545453 which advises to run program in se38
K_REMOVE_DOUBLES_FROM_STD_HIER
I did this and it removed my duplicate groups and doing the ambiguity checks again passed.
This program solved my issue in live system.
Regards
Amer