Your surprise comes from a perspective of understanding and trusting the process, presumably from experience. Is it really such a surprise that someone with a different experience -- that of extending trust and having it betrayed -- would find it hard to extend trust a second time?
And yeah, this system seems to be the worst of all worlds: needlessly punishing for small players and needlessly lucrative for large ones.
The patent system, as it is implemented, clearly behaves as an instrument of power, not an instrument for fixing incentives.