I’m having the same issues with the cross dissolve not importing from a Premiere Pro project. And I have the same version:
PremPro: 4.2.1
AFX: 9.0.2.42
Matrox RT.X2 with driver version 4.1
The clips overlap once they are imported into afx, but the opacity keyframes do not change. This bug occurs with dissolves of all different transition lengths, and I have tried it with MXF’s, MPG’s, and AVI’s and still get the same results.
Any new thoughts? I guess I’ll do the bug report too…