Probably the desk? - BUT - you can experience this if using mix windows in certain configurations.
What is your screen configuration - ie mixes, overlaps etc?
There is a setting in the 'Mix Options' to change blend glitch: A / B / C
Try changing the setting from what you have now and see if the crossfade changes.
Best test is to use 2x white layers - and x-fade between the two (2sec) - this is really where you will see any difference.
If you have the correct blend glitch selected - you wont be able to see the crossfade between the white layers.
To identify if its the desk - create 2 presets in catalyst to do the same thing:
Use 2x white layers - and x-fade (2sec) between the two
If it works fine with a preset and not over DMX from the desk - then it's probably the desk...
Else - check / change the blending glitch for those mixes in use.
Blend Glitch can change the way in which some colour fx work - so do check carefully.
Simon