I'm having the same problem, I've got lscolor loading first and then all my non-visual modules, then grdmagick and then the modules I want to change the colours for.

*NetLoadModule lscolor-1.5
*NetLoadModule mzscript-0.9-beta_12
*NetLoadModule desktop2-2.0
*NetLoadModule grdmagick-1.3.1
*NetLoadModule popup2-2.1.4
*NetLoadModule vtray-1.05
*NetLoadModule taskbar3-0.306_alpha-3
*NetLoadModule lsxcommand-1.8.5
*NetLoadModule shortcut2-2.0.1
*NetLoadModule label-1.99

Then I'm trying to use it like this:
*grdMagick label-1.99 replace 0xFF7FFF 0x000000