Hello,
The issue is that we only read the target options from the registry at startup and then we use a local copy inside our library. Whenever you change the target options dialog and select OK we update the local copy and the registry but we don't read from the registry each time it is opened. I have not looked at Blackfin but based on what Craig did it sounds like we may read from the registry each time the dialog is opened. So by using the script, it updates the registry but the dialog does not have any idea as it is working off the local copy. To fix your issue, you could remove the breakpoint prior to running so it does not hit it again. Or you could update the register to mask interrupts, step, enable interrupts and then run. I know these are not ideal but it should be a way around this.
Regards,
Chad