My initial project for them was an eternal struggle to get basic things (XML parsing, Hibernate, CDI, etc) working in their environment because specific versions of these things were already included in the app server, and always ended up conflicting with libs we needed to include for our own app. I remember it distinctly as one of those times where I just felt helpless to make anything work.
The startup was already on its last legs at that point, as I was the only active developer since the other developer I worked with had already left after getting fed up for other reasons. After I left the startup limped along for a while but as far as I can tell was abandoned. If they had just used a more sane environment I could have easily developed the entire thing myself as it wasn't anything more complicated than a straightforward CMS + payments. I still kick myself for not making a better case for a more sane environment but I was wet behind the ears at the time and I didn't trust my instincts in the face of guys with masters degrees and X years at IBM and other top companies. I know better now.