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However, that isn't Samsung Magician itself, but rather a side feature it has. Forces the SSD to use Real Time Acceleration Processing of I/O Data. For benchmarking it appears good, but actually in real-world performance, just slows down your boot, adds another background process, and doesn't speed up game performance or anything majorly useful. It's a have, and personally I see little to no point in using it, other than to give a faked illusion of more performance (which happens to be more unstable as well on quite a few system, which is why they leave it disabled as default).
I use Samsung Magician on a 850 PRO SSD and have never had any issues, except I don't use the Rapid Mode on it. If you want to reinstall it, check if that is on or not. Disable it if it is, as that's an active task which would affect the entire system.
There's no only reason I can think of which would affect your system that way, by just having Samsung Magician running in background.
I have a Samsung 850 EVO 500GB. I've only had it for about 2mths.
I think it was the cause of the problems because after un-installing Magician, everythink seems ok again.
Fully uninstalling the Samsung Magician software would of also disabled it.
In which case, just reinstall and disable that feature. You should be able to still use the rest, if desired.