[galaxy-user] problems in transitioning from Tophat to Cuffdiff

After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy. I had this problem with histories developed before the move and histories developed after the move. I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC. I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories. Is anyone else having this problem? And found a solution? Elwood Linney