Was this ever resolved? I'm having the same issue. I have three PCs. When the two secondaries are on either side of the primary (S1PS2, see first image below), it works fine. But when I move the right secondary (S2) to the left of the left secondary (S2S1P, see second image below), the cursor is always at the bottom of the destination screen when moving from S1 to S2 (or vice versa).
After playing with it a bit, I find that cross-screen mouse cursor alignment only works between primary and secondary. If two secondaries are placed side by side, the problem occurs between them.
I'm using Multiplicity Version 3.57 Build 00103.