Yes, you can configure the vertical reference delay in the Hardware Setup menu for the matrox. The proper settings are all depending on whether you are using Trilevel Sync or Blackburst and which video format you are using.
Assuming Trilevel sync and 1080i, try setting the vertical timing offset to 1124.
If using blackburst sync and 1080i, try setting the vertical timing to -2.

#XPression