So I'm using QIIME 1.8.0 with the script "group_significance.py", this script should allow me to do multi-variate analysis, however, not matter what I do to the associated mapping/metadata file (which is validated) I can only attain statistical scores for 3 variables...

I wasn't sure if this was because they were the 3 most significant differences (out of the possible 6 variables), but reading the literature it clearly states that there should be means for each variable detected in the column.

QIIME script page: http://qiime.org/scripts/group_significance.html