jungleJollies: Not sure how specific this is to my save files; if needed I can send them your way.
I am on the island, after gleaning the relevant information about ths shot trajectory.
As I return, I get a purple circle. I try to save before entering the door back into the fort (control pannel area).
The save fails: it gets stuck in the three dot loading information and the file I was saving to becomes lost.
Tested save feature after re-entering the control room; saved as normal... so location appears to matter. Tested the fail conditions twice, they happened both times... then I applied a skill point (following learning the miracle and whatever skill you pick up after talking to the dice girl) and it crashed on the save again.
Similar weird issue... killing time to get my last perks before opening the door. Reading through my ledger, at the "Fall Sideways" option, the game just restarts -- as in, title screen, ancient reptilian brain "begin". Not sure if it matters, but I did this option inside the control room after the above mentioned stuff was done.
I actually wasn't able to save AT ALL once I stepped onto the jetty, just before heading to the island. From that point on till the end of the game, the save was dimmed and quick save didn't do anything any more. I thought it was a "feature" so plowed through till the end of the game - which was a fair few hours!
By the time I realised that it probably wasn't supposed to stop me from saving all that time, I'd gone too far to stop so figured I might as well ride it out till the end.
I suspect this (and possibly your issue) could be related to how long the play session has gone on? Either that or saving gets really funky near the end (and not in a good way).
I'm pretty sure some of the bonuses from thoughts don't actually work. Examples include the 10XP bonuses you get when you have the "Actual art degree", plus some others I can't quite place.
I THINK the ultra-liberal stuff works though.
Also you don't seem to get the bonuses from certain "thoughts" if those thoughts were applied from clothing, but that could be by design. I suspect that they only raise your fascist/ultra-liberal/moralist/communist rating when you wear them (though not sure if it's applied just the first time you put them on, or if it's regularly at certain time intervals while wearing them).