Yes, there's something wrong, but it's my fault, I didn't document the filter properly : coefficients have to be separated by spaces, not comma.
Anyway, here's a new version, which can load CQM matrices :
http://manao4.free.fr/AVCMatrices-1.1.zip
Oh, and to finish the undocumented 'features', if you want to do a test without CQM, but with PFrames, you'll have to give at least one flat P-matrix, else the filter will encode with only IFrames.