Considering that PTSC has been upstaged on every negotiation they have been involved in so far, it isn't surprising that TPL tried to take advantage of PTSC. Perhaps it took TPL defaulting on repayment of the loan for PTSC to finally question TPL's licensing activity. Perhaps PTSC thought that this could put more pressure on TPL and could result in a more favorable agreement for PTSC between the two companies ie more PTSC involvement and say in the MMP licensing activity.
I do think that the 336 patent was significantly strengthened by the USPTO recertification and that going forward now infringers will have a more difficult time trying to evade payment and ultimately should pay a higher fee. The only question I have now is is TPL in such poor shape financially that they have lost some or most of their ability to pursue licensing? It would appear that with them not paying Moore and borrowing from PTSC and defaulting on that loan seems to indicate they are in trouble.