It only appears to happen with some existing ioc files. It doesn't happen with a new file, but I haven't looked into if I can replicate the behavior from a new file.
The issue happens when I open the NVIC panel and then immediately generate code (it doesn't matter if I click anything after opening the panel). The ioc file then gets modified to delete the timebase timer interrupt, but the NVIC panel itself doesn't change. The generated code then removes the interrupt configuration, which causes the program to get stuck because the timebase timer isn't fully setup (or something like that). I can't reenable the interrupt because the config window doesn't allow (de)selection of the timebase interrupt. Changing the timebase timer also doesn't enable the associated interrupt, so I have to manually re-add the interrupt configuration by directly editing the ioc file in a text editor.
I did notice that selecting an NVIC tab in a specific peripheral's configuration panel (vs. the main NVIC panel under System Core) doesn't cause the issue.
Again, not certain that it is specifically some interaction with the timerbase timer causing the issue, but I haven't had the issue with anything else so far.
