Infinite loop between JTAG and ISR

I've got a design with 3 cpu's running, each with their own jtag instance. One of them is working nicely and perfectly, but the other two (seen through debugging) loop continually between the JTAG IRQ handling code and the default ISR. The JTAG code checks internal JTAG values to see whether it needs to handle the IRQ, and sees it has nothing to do. The IRQ is however still active, so the ISR loops back, resulting in an infinite loop. This happens at a random point in time after starting the design.

Is this a familiar problem and/or does anybody have a solution?

Thanks in advance.

The board it's running on is a Stratix II development kit.