The problem is perhaps what you are expecting...
If the yield is higher, this doesn't mean that the PR is higher, as it is normalized to the installed PNom. If the PV modules have rigorously identical performances (same Low-light behavior, same temperature coefficient, same IAM), the PR should be identical
Now you don't tell us which level of differences you observe (in percentage).
There may be a discrepancy:
- If you have inverter overload: in this case the loss will be higher for the second system, and therefore the PR will be lower.
- As explained in the FAQ Why is the Pmpp of my modules different from the specified value?
, the Imp*Vmp at STC may be different from the PNom of the module. This will induce a distortion of the PR.