Dear Joshua,
Thank you for highlighting this and providing the details. Is that 55 hits or 55 hit sequences each with potentially hundreds of HSPs (local pairwise alignments)?
FWIW, the way we parse and return results is completely rewritten in version 2, in part because of performance/scaling issues.
Our version 2 "prereleases" are actually very stable (we use them for research, but have conservatively stopped short of calling them completely stable because we're still ironing out a few details).
It would be super helpful if you could try running your analysis in v2 and let us know if you get the same pattern.
Yannick