Err, 1) Shield of Illmater?
You mean the Holy Buckler of Amaunator +2?
If so, I believe that was kinda intentional. Only Cespy can do the Holy Buckler upgrade (losing the Symbol of Amaunator before rescueing your romance/Solaufein == teh bad).
Hmm although it appears it does allow this.
Odd, the latest version should create trigger the buckler option (blah blah this forlorn buckler) when you have the buckler.
The other problems are actually results of it installing over itself, instead of being reinstalled. Usually results from some files being write protected at the wrong time, best suggestion is to do a fresh install (delete the override directory, chitin.key and bgmain.exe as well).