Ok, I'm almost certain as to why this happens, because it happened to me too recently. I believe the culprit is a failed (or incomplete) Windows Update. In my case, I stopped the mistakenly running Windows Update process by turning off the computer, and that resulted in an incomplete update and some "errors". The effect on Rainmeter in my case was that while Rainmeter itself could run if was previously deleted or the default one with the Illustro skin, as soon as I tried to load skins using the UsageMonitor plugin, the notification area icon would dissapear and Rainmeter would silently crash and "unload" from the system tray. Another issue was I had a error when trying to start Windows' Event Viewer. I played with the permissions and managed to replace that DLL (both the 32bit and the 64bit one), but while Event Viewer didn't yeild the error anymore, it idn't fully solve the issue. The fix was to run the SFC command above in order to restore my previous Windows files (from before the failed update).
Now I'm not suggesting you try this too, since your scenario might be different from mine (e.g. different Windows DLL dependencies of Rainmeter or its plugins, etc.), I'm just sharing my own experience in a similar problem - maybe it helps you somehow.