I guess it is just a problem for my set up, so I won't take up any more of your time. Thank you for looking at it.

If I figure out that there is a conflicting program, I'll post again.

I tried another option in Advanced Options and that worked.

I've had a quick play around and the issue might be that tray_icons_padding will take effect if the change to the value is large enough? 

For example, if I start with 1 and change to 5, there is no effect, but if I change from 1 to 10, and then to 5, it seems to work.

At least I can get it do do what I want now. There is just an extra step.

To add to my OP, it looks like it takes effect sometimes. I had it work at 1 (too close), and then 50 (too far), but now I changing the number has no effect again. I don't know what is different.