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Interrupts while booting from bank 1

Hi,
I'm using an STR912FAW44 and am having trouble getting interrupts working when booting from bank 1.

I need to have the device booting into bank 1 (32kB) where a bootloader can run an application in bank 0 (if one exists) or be used to programme or update one if necessary.

I have an app that boots into bank 1 (remapped as per instructions in article 3347) and can erase and write to any of the 8 sectors in bank 0. However, when I try to configure timer 0 output compare to act as a 1ms timer it only enters the TIM0 interrupt once. The timer configuration and interrupt handling code is taken from another app which works running in bank 0 with the default flash configuration (boot to bank 0 at 0x00000000).

Does anyone have any ideas where I might be going wrong?