I found your problematic jobs.
The root of the issue is a chromosome identifier mismatch between the custom genome used for mapping and the reference annotation GFF3 dataset.
The custom genome fasta (single sequence) has a title line in this format:
>gi|116048575|ref|NC_008463|pseudocap|138 [Pseudomonas aeruginosa UCBPP-PA14 chromosome, complete genome.]
The reference GFF3 has the chromosome identifier with this content:
Both must be an exact match when using most tools, including Cuffdiff. You'll need to edit the fasta to have this content (only) in the fasta title line:
This can be done in Galaxy (using Text Manipulation tools, as NormalizeFasta will not be enough for this data content) or edited prior to Upload to Galaxy. Once fixed, rerun the mapping jobs, then downstream tools.
Thanks! Jen, Galaxy team