I am wondering why Cuffdiff suddenly gives many more significant DE genes?

Cuffdiff was recently updated to version 2.1.0; this update likely explains the different results that you see.

I have rerun several analysis, also with more samples in each group, all give much more significant genes. Why?

More samples = more power to accurately estimate expression levels = more DE genes.

Also, will replicate information soon be included in output files?

Replicate data will be available when we next update our server. This should occur in about 3 weeks.

Best,