I deleted the old folder and all remnants of the prior installation. The "war is over" bug surfaced for me last week after patrol 1 of this career (#2).. see my posting
http://www.subsim.com/radioroom/showthread.php?t=127100
I had a helluva time saving the career and then it stated in SH3 commander that I was retired but i managed to return to duty. The first career i started with GWX 2 went great, until i returned to port and went to play the next day and my saves were empty. I did read on a forum how to get around that bug, but didn't know it at the time, so i just restarted. Seems i'm just having a lot of issues that i didn't have when i had GWX 1.2 loaded prior to this.
Tool.