I finally found one way to fix the problem.
That is, using old version of polyphone.
I installed 32bit polyphone 2.0.1 in windows10 PC(64 bit system) and this works very fine. It did not add any modification to samples when I imported samples or saved and loaded soundfont.
(I hoped something was changed when I installed the old version and tried the procedure once again in 2.5.1, but the outcome was not changed.)
Although I can not have any idea what is wrong with my 2.5.1 and my computer, this is a very good progress for me.
I have two more news.
Firstly, 64bit polyphone 2.0.1 after I uninstalled 2.5.1 works fine as well in my windows 10 PC.
I worked with that these 3 days and confirmed several times but the phenomena was not occurred.
And also, polyphone 2.6.0 BETA in my windows10 worked fine! No additional noises when saved, loaded, and imported the samples(soundfont).
To confirm whether the version difference, or reinstall solved the problem, I again uninstalled all the polyphone in my windows10 PC, rebooted PC, and installed again 2.5.1 from newly downloaded installer.
Again, I confirmed that 2.5.1 added modifications to samples when imported the soundfont, and saved(or loaded) the soundfont.
It may be that my two PC(windows10 and windows11) has something that interact specifically with 2.5.1.
Although the phenomena is environment-dependent(confirmed by bottrop's investigation), and the trigger is unknown, I am afraid that the trigger is rather common(including my possible oversight), because it reproduced in my two very different computer(windows 10 and 11, notebook and desktop and has different audio system), and even after reinstall.
But anyway, now I hope the solution is very simple.
Just update to polyphone 2.6.0 BETA.
I will confirm whether 2.6.0 BETA actually always works fine.