I looked up Wallch just to find out a little more about it-
It might be conflicting with Compiz Fusion.
One reason (I think) it's Compiz) is conflicting with Wallch is because Compiz pretty much for the most part communicates with the Gnome Desktop and it's functionalities.
Compiz is buggy with Ubuntu; I know because it used to be my primary OS but I'm not sure about Linux Mint-
You should be able to use your Synaptic Package Manager but you mentioned you can only do so in Mate mode-
I found this article at www.linuxmint.com
Wallch doesn't work in MATE. There are similar programs in the repos: desktopnova or cortina. None of them work properly in gnome shell, but both of them used to work in gnome 2, so you can download them and give them a go
I'd do more re-search to see if others have found a way around the circumstances.
Other than this the only other thing I can suggest is to tweak the configuration file for the wallpaper changer or perhaps write a shell script that could modify what would make the change you need if applicable-
I'm still learning so shell scripting to run a job isn't my speciality as of yet-
Took at shot at this hope this helps