Partial amount picked up in payment run(t.code F110)

Hello guru's,

I am facing strange problem in payment run.I have two invoices($10000+ $5000) due in one vendor account.when run the payemnt program. system clears the both documents but with differnt amount $3000. Hence, cheque was issued to vendor for $3000 rather than $15000. There are no credit notes are pending againt this vendor.It's production issue, please suggest me on priority.

Suitable answers would be rewarded.

thanks