This issue can happen in a Vivado 2013.3 Xilkernel design that is using the interrupt controller.
If I set breakpoints in the xmk_add_static_thread, then run the debugger with Launch on the hardware (System Debugger), breakpoints set in this thread are not triggered.
GPIOs written from within this thread do not have any effect, and the thread never seems to start.
This issue is fixed in SDK 2013.4.
For SDK 2013.3, you can work around the problem in GDB by using Run As (Launch on Hardware (GDB).
If you need to use SDK 2013.3 and System debugger, you can do the following:
hw_server s tcp::3122