Yes this is partly linked to a known issue that I've just discussed with Marian, see the following ticket:

https://gna.org/bugs/?17228

I wrote some ideas to solve it. However if you change resolution using the graphical tool lxrandr, I'm not sure it records the new resolution in a configuration file. It may only invoke the underlying xrandr command to change resolution on the fly. In this case we would need to add a script at shutdown that modifies the Xorg configuration file using the current screen resolution.

Concerning mouse setting, if you run the CD with persistence activated, it should be retrieved after rebooting whatever the type of persistence. Setting is recorded in the user's file “~/.config/mouse”. You may check the content of this file.

NB: testing persistence of settings should be part of the testing process for your students.