It is difficult to change the paths to BuildWrapper and ScionBrowser. The browser feature doesn't seem to work - you can browse to another file but the change won't be reflected. It seems like you have to uncheck the cabal file (circled at the top) and then type or paste the paths in to the executables rather than browsing for them. Then you have to recheck the executable so save them.
Skitched up screen cap showing paths hard to edit.
I can't reproduce. You're using 2.2.3, right? I can change the location of the executables via the browse or the autodetect button and the change is always reflected fine. Any error in the Eclipse log?