I suspect it is a combination of both...an unfortunate marriage of a genetic susceptibility and the PANDAS-related inflammatory response. And it may not be a "flare" so much as a continuation of the original PANDAs/PANS immune onslaught; many of us find that a "typical" or shorter course of antibiotics is insufficient for fully addressing our kids' conditions, so a two-week course may not have fully addressed the "animal" that is PANDAS/PANs.
Our DS, too, had some mild sensory issues prior to a the full-blown PANDAs episode that sent us into a tailspin. Once the PANDAs hit full force, we had him professionally evaluated and as with most of his behavior set, the results came back "borderline." During PANDAs, he was alternately identified as "borderline" a number of things: OCD, Asperger's, PDD-NOS, Sensory Processing Disorder. You name it, the poor kid, at one point in time or another, wore a label for it.
What I can tell you is that, with the conclusion of effective PANDAs treatment, the sensory and social issues resolved 100%. One doctor even took steps to revise his file to remove the former ASD notation he'd made there.
I would say, however, that I don't think you are wasting any effort in giving her access to OT; I think it will only help her as she heals and enforce positive behaviors and coping strategies that will stand her in good stead going forward.
All the best!