It is probable that the 6x6 are pulling down the 5x5....not the other way around...... why?
I suspect your 6x6 run at a lower voltage than the 5x5 panels. As a generality, the 6x6 cell 250w panels are 60 cells ( 30x 2 for 12v panels) and the 5x5 cell 72 cells ( 36 x 2 for 12v panels).......or even some other combo.......... Same watts, but different current and voltage to get the same watts.... count the cells in each type of panel.
If the cell count ( or the Voc from the sticker) in the 5x5 is the same as the 6x6, then no loss of watts in the parallel connection as the Voc is the same..... if different ( Voc is different)...... then you will do a bit better if you match them up as you suggest... 5x5 together and 6x6 together to independent inverters.
More in depth understanding of solar panels can be obtained here also in a series I wrote on another site
http://www.fieldlines.com/index.php/topic,145005.0.html..................oztules