Freezing, Ink, and Desktop Messed Up?

[Chris Stormshot]

Ok, so there are three problems I experience constantly when playing POTCO.
1. ESPECIALLY when sailing and battling at seas, the game freezes constantly, often meaning my enemy gets away. Is there a way to remedy this?
These next two, out of general note, happen when I exit the game:
2. Whenever exiting, Mac OS X's "Ink" application made for Wacom tablets always pops up. I have a Wacom, but I always keep "Ink" closed, and it is a little annoying to have it pop up all the time...
3. Whenever exiting, the desktop icons scramble. This is a very short lived glitch, but it can be annoying.

I'm just making sure that none of these are problematic, and I was wondering if there is a way to fix them. (ESPECIALLY the first one.)
Thanks,
CS~