Hi Mike,
just had a play. The gui install does seem broken and I have mentioned it on a rpi forum. I used sudo apt-get install ./progname.deb to install both wsjtx and spark, I believe this is a modern extension of apt-get that also gets the dependencies.
I don't see the wsjtx issue, maybe because I installed it first, spark tries two locations for the files on the first go, after that it uses the location stored and displayed in settings which will be the last placed tried if not found.
I've not managed to make favourites fail but I know there was something odd on 2.0.33 and before that made them disappear when the theme was changed, this was fixed in later versions so hopefully will also have also fixed your issue.
I found something else odd, on a 7" screen the app starts bigger than the screen and you can't get to the window size controls, a work around is to press ctrl-alt-left arrow and then resize it.
Thanks for the heads up.
73 Alan M0NNB