This type of inconsistency between IT 2001 & 2006 happens sometimes.
To resolve this:
1. Run RPTKOK00 for the employee (in sel.options, you may remove the default for emp.status not 0)
2. If it lists any inconsistencies, it will provide an option to correct. Choose the option and it goes to execute RPTBPC10.
3. Else the easiest way to correct inconsistencies in leave deduction is to delete an existing absence record and create a new one, or, for a deduction without an absence record, to create an absence for the period and delete it again later.