Well, this are two interesting issue I'm currently facing, while handling the general i/o ports:
The required pins are configured as digital and push-pull modes.
Could I ask a question? Which device you are using? are you working on a board self-made by yourself or a DK barod from Silabs?
for trial i used the example for port I/O with minor tweaking. I attach my schema and the code in attachment.
I did not see anything wrong in your attached code, but I prefer you could upload the code that blink p1.3 that you think not working as you have expected.
In the attached code I did not see any code that operate/toggle P1.3.
On the F350 TB board there is no problem to toggle the P1.3.
I tried attached code with simplicity studio.
I also tried to toggle p0.0, could not reproduce the issue you observed.
Change the LED2 to P0.0 in the attached code to test the P0.0 toggle.