the problem is that active processes such as crop and DBE 'do something' when you click in an image. So it's not a 'free' operation.
When a dynamic interface is active you can select the readout mode (Alt+R). To continue the dynamic operation you can select the dynamic mode (Alt+D).
In addition, you can set a STF to darken the image slightly. In this way the cursor will be well visible.
I'm assuming the cursor color gets set by the graphics hardware, right?
Not in PixInsight. Everything on the GUI is drawn without the help of any OS resources, other than those necessary to build pixmaps and draw them on the screen.
For this reason we can solve this issue changing the cursor color through preferences and, when I implement it, through a set of dedicated options. Benefits of platform independence
By the way, you asked about changing preferences not working - remember that you must execute the Preferences process globally (F6).