I am using the latest Beta version (126.96.36.19908), though i was paying extra attention to the hidden startup folders before/after reinstallations!
Nothing was there, all the startup folders were empty and remained like that.
I don't think Rainmeter is responsible for this phenomena.
So far, since i removed the "leftover" files with that uninstaller program, the issue is gone now, and did not returned.
So i think the problem is with windows. Maybe some update made some registry entry or other thing, which wasn't directly connected with Rainmeter and it's uninstaller, so it remained hidden and left back. And with a simple reinstall process it activated again as a Bug in windows.
My thinking was based on that is Rainmeter wasn't launched when the system started up, it launched when i connected to power. Without connected, it did not started, but with connected it started at the time of connection/or connected starting up.
That smells like...windows spirit.