IIRC they had a blog post up about their brilliant NIH Javascript UI framework and if you are familiar with that kind of thing you could read between the lines and generate some good guesses about what was wrong with it.
Not that Jira is a ton better, especially with each heavier-and-worse-than-the-last redesign. Friggin' "web apps".
[EDIT] and for all that the workflow wasn't any better than anything else as far as I could tell. Our PMs who lived in it loved the draggy-droppy interface and hotkey-heavy workflow, but again, everyone (of their competitors) has that too. To me it always felt like working on someone else's messy desktop shared over VNC. I was afraid to touch anything for fear of accidentally performing some kind of write operation without noticing, and fucking things up.