I kinda have the feeling. It was pretty sever (and seemingly random) when introduced but got better with 1.6.3 (or maybe I was just lucky for a while?)
But now in 1.8 it seems kinda random and crazy again, I'm playing Theodoro any my allies are (were) Muscovy (not Russia!) and Poland-Lithuania. Muscovy already broke the alliance twice because of -200 WYP and entered it again, a third time I could hold the alliance at +3 relations (with -200 WYP) and via a war I kept them positive for a few months and suddenly WYP was gone again and alliance was secure. (Currently they have formed Russia and WYP is interesting enough a little lower , -173, but doesn't seem to vanish again, but since they have now claims on many of my provinces that's not too surprising).
Poland-Lithuania was similar but less hard, stable for most of the time but then again for a few monts about -160 or so WYP, luckily not enough to break alliance and suddenly gone again.
But now in 1.8 it seems kinda random and crazy again, I'm playing Theodoro any my allies are (were) Muscovy (not Russia!) and Poland-Lithuania. Muscovy already broke the alliance twice because of -200 WYP and entered it again, a third time I could hold the alliance at +3 relations (with -200 WYP) and via a war I kept them positive for a few months and suddenly WYP was gone again and alliance was secure. (Currently they have formed Russia and WYP is interesting enough a little lower , -173, but doesn't seem to vanish again, but since they have now claims on many of my provinces that's not too surprising).
Poland-Lithuania was similar but less hard, stable for most of the time but then again for a few monts about -160 or so WYP, luckily not enough to break alliance and suddenly gone again.