The following post will hopefully give some insight into an installation from Steam concerning the Program Files issues:
https://www.subsim.com/radioroom/sho...01&postcount=4
Secondly, the stuck on pause issue is generally caused by a corrupted main.cfg file located in the Documents/SH3 folder, specifically regarding the time compression settings. See here for more info and the solution:
https://www.subsim.com/radioroom/sho...d.php?t=253110
Good luck,