Sorry for the thread necromancy, but I am having sort of the same problem.
I am using the Minimalsim Theme and I am having a problem with the rainmeter bar at the top. Whenever I go into a fullmode program, the bar at the top stays in view and flickers alot. I found all the threads saying change the AlwaysOnTop to false, but in this config file it used numbers. I went into the help file and found the settings for that command and tried all of them, none fixed the problem. I even tried changing it to "FALSE" even though that isn't stated as a valid option. I think it is a problem with the way the bar is refreshed, thus creating the flickering.
The HideOnMouseOver command works if I turn it on, when I am in the program and mouse over it, it will dissapear after a second or so. It is still annoying though, with the flickering and all. If I turn the bar off everything is fine, but I would like to be able to use fullscreen programs without having to turn on and off the bar every time I go in/out of them.
I looked in the thread for the theme itself and they didn't have anything about this problem. I did a search for "rainmeter flickering" and didn't come up with anything, so I am sorry if this is a easily fixed problem but I can't figure it out, and the only answer offered anywhere is the AlwaysOnTop command, which isn't working.
If you can help thank you very much. I am using rainmeter .13 with explorer as the shell. The minimalism theme is here:
Edit: It is kind of nice being able to see what song is playing/the computer stats. If there is a way to get rid of the flickering, or to make it so it wont intefere with the program being run that would be cool as well as fixing the alwaysontop problem.