Hi
I just checked your subject of topic. It is saying you are not able to apply leave from R/3 as well. In this case, the issue will not be from documents.
There must be black quota issue here. Can you check if there are some quota which is not valid for employee, is still there. It happens when employee's EG/ESG or PA/PSA changes, which changes quota eligibility.
Run report RPTKOK00 to see if there is quota inconsistency.
Regards
Aj