The on-screen indicators for Key Maps and Repeater are menus, not clickbars, so you may be attempting to save those on the wrong tab of the ISBoxer Control Panel.

For Video FX, the procedure for saving a set of Video FX viewers and sources (and having it auto-load) is to type "Auto" (should be there by default) in the Save As box, and hit Save As. Any other name will not auto-load but will require a Mapped Key with a Video FX Action to be run from your ISBoxer profile. You could create a couple of different Video FX Sets in the ISBoxer Control Panel and switch between them (select the Video FX Set from the dropdown and hit Load) to confirm your changes are being saved.

You can confirm for yourself that settings have been saved by looking at the files created in the InnerSpace/Scripts folder. Files have the naming scheme ISBoxer.(interface element).(character set).(character).XML. Note that VideoFX appear as VideoFeeds (the older name).

Finally, the positions of menus (by simply setting starting position) and Video FX (using VideoFX actions) can be specified from within your ISBoxer profile if you wish to go that route. For the latter, MiRai has a recent series of videos which cover this feature.