Tonight on 27th of June at about 3 AM (GMT) I played against MMP66 and was queen and 2 pawns up against my opponent's king only when I ran out of time... results: lost game and 21 points lost in G5 game.
I believe on CaissaClassic this would have been scored as a draw because of no mating material. Will this be handled differently in future?

AIUI, the "no mating material" rule means that neither side has a set of pieces that can possibly lead to a win. At least in standard terminology. You had more than enough material to win, you just didn't have the time.
 
However, in competitive chess, there's a rule (don't know if it's universal) whereby if you have less than 2 minutes left and your opponent can't possibly win by any sequence of legal moves, you can claim a draw. Or something like that. What Caissa lacks is this rule.

FIDE Laws of Chess
9.6 The game is drawn when a position is reached from which a checkmate cannot occur by any possible series of legal moves, even with the most unskilled play. This immediately ends the game, provided that the move producing this position was legal.

I'll have to check the status of this, but if it is not already, there should be some basic functionality in the new Caissa to offer a draw in the case of no mating material. Thanks for the report.