If two timers generate interrupt at the same time, xps_timer generates the interrupt signal only once. Even if one of the interrupt status would be cleared and another status remains high, the xps_timer never generates an interrupt signal.
To work around this issue, when two timers generate interrupt at the same time, both of the interrupts (status) must to be cleared in the interrupt handler.
This issue will be fixed in the AXI Timer, but is currently not planned to be fixed in XPS_Timer. The AXI Timer fix is currently planned to be released starting in EDK 13.2.