"Generate Output Products" is not running when some Isolation Configuration parameters are changed.
One symptom is that psu_init.c (included in the .HDF file exported to XSDK) is NOT updated to reflect the changes done in the Isolation Configuration tab.
Please note that the problem is restricted to some Isolation Configuration parameters only.
If any other parameter gets modified, it causes the "Generate Output Products" to be run.
The work-around is to select "Reset Output Products" and then "Generate Output Products" again.
This issue is planned to be fixed in the 2017.4 release.