Did you get your answer on this? I can probably help there if it's still needed.
Meanwhile, to the others on this thread, I apologize for piling on an aging forum thread, but I too have had issues with interrupts and using the UIO driver. I have been using the UIO driver to provide various interrupts (from the PL of the Zynq) to the PS. I have a handful of threads that are invoked from my application. For whatever reason, I slip/miss interrupts on occasion (several in a row for that matter). I lack the in-depth understanding of the linux kernel and the UIO driver. Both would probably make troubleshooting a little easier. Still, I blame either the UIO driver or how I am using the driver to poll for interrupts. Is anyone else using multiple interrupts with the UIO driver? Is anyone else having problems missing interrupts? If anyone reading this can help, let me know. I would be more than happy to provide additional information about what I am doing and the problem(s) I am experiencing.