Hi SentaiBrad, Thanks for responding to my question. Love the YT vids btw. Here are a couple things I tried:
Tried other DOS only games (no sourceport, first tab path is directly to DOS exe, dosbox checked under dosbox tab). Success.
Created a test Doom II entry (DOS version first, first tab path is directly to DOS exe, dosbox checked under dosbox tab, sourceport version under additional apps). Success.
Tried other games where sourceport version is first and DOS version is under additional apps. Same failure.
Since these were working before, it lead me to believe that apps under the additional apps tab were now keeping the root folder value under the folder tab instead of only using the additional apps application path.