the program doesn't return from interrupt

Are you using your own interrupt handler or the one from the HAL?

The HAL UART driver clears the interrupt in the function alt_avalon_uart_irq before processing it.

But it is possible that if you're single stepping then the hardware will have interrupted again before you have stepped out of the interrupt routine. For example, if transmit interrupts are enabled then it will take a few ms to send the characters which have been queued up, but several tens of seconds for you to step out of the interrupt routine.

One thing I notice when stepping through interrupt routines is that the timer interrupt is almost always set (since it takes more than 10ms for me to step a few times). I solve this by stepping out of alt_irq_handler using the step out button rather than one line at a time.