Diff between kernel configs is in the attachment. I noticed that CONFIG_DRM_DIGILENT_ENCODER option is not set in Digilent kernel config, and it is set to "y" in Petalinux kernel config which works. Perhaps that is the problem?
Device trees are very different and there are several files so I did not do a diff between them, I attached all of them in the tar if you wanted to take a look.
Another question, when using Petalinux with Linaro Gnome (Ubunutu version 15.04, downloaded from here), I can only get console output and not GUI. I try to start gdm but nothing happens, and thi