It gets really tedious as it basically means I have to reinstall Uashell each time I want to play or simply reload a savefile.
I'm glad you have a work around for now. My laptop uses Windows 8.1 and UAShell works normally on it.
What I do:
1) Start DOSBox by double-clicking.
2) Type in "UAShell" which leads to a message "GAME02.DSN successfully applied." Press OK.
3) Press F8 to start the adventure. Have fun.
4) At some point, Encamp/Save/Game A/Quit. "Return to Reality?" Yes.
5) This leads UAShell to repeat itself "GAME02.DSN successfully applied." Press OK.
6) Press Alt-X to Exit. (You can also go to the Design menu and pick Exit).
7) Type "Exit" to quit DOSBox.
I mention the above in case you are trying to Exit UAShell by clicking the big red X in the top right corner. This would terminate the batch file in an unexpected way, possibly leaving files in your TEMP folder.