partial payment and general ledger

when I make a partial payment of an invoice, it records the amount in the GL slightly out by a few cents -why??-i.e. I recorded a payment of 1100 for a yearly invoice totallying 13200- in GL it shows in the income account there is an entry of 1000.08 and gst amount of 99.96 however the gst detailed report shows it correctly being a payment of 1000 with gst of 100