as suggested here in a previous question (here), I used TRANSFAC2MEME to convert a minimal TRANSFAC PSSM into a MEME one. Since I generate by my self the TRANSFAC matrices, I cannot provide the program additional information beside the name of the matrix and the matrix itself. The MEME format is more informative than a TRANSFAC, and I feel this to be related on my failure.
From MS-DOS Prompt I obtain this:
C:\Documents and Settings\Standard\Desktop>perl transfac2meme.pl rax.txt MEME version 3.0
strands: + -
Background letter frequencies (from dataset with add-one prior applied): A 0.250000 C 0.250000 G 0.250000 T 0.250000
Converted 0 motifs. Skipped 0 motifs.