i might have a clue...
think it has to do with the fact that your BasePR doesn`t get calculated at every turn.
did you populated /build a lot on your colonies after ( logging in OR building any ship OR plundering )?
that would`ve mean that your basePR had augmented, without it actually being recalculated and adjusted in your totalPR
then, when you got attacked i suppose it went like this:
NewPR = OldPR - ( FleetPR lost in attack + PR of lost colonies )
and because the oldPR didn`t included the high pr of your colonies lost, it went below zero.
just my attempt for an explanation,
someone should test this.