M569 (StealthChop) commands are reversed.
Marlin 2.0.5.3 with SKR Mini E3 configurations, mostly from
https://github.com/morningreis/Marlin-SKR-E3-Mini-1.2
Expected behavior:
The reverse of above
Actual behavior: [What actually happens]
Here are screens of the error


Seems like other people are experiencing similar. Here are 3 reddit posts about it.
https://www.reddit.com/r/ender3/comments/gdmn65/stealthchop_gets_disabled_every_time_i_reboot_my/
https://www.reddit.com/r/3Dprinting/comments/g8gu9s/marlin_20_skr_mini_e3_stealthchop_issue/
https://www.reddit.com/r/ender3/comments/gev9f7/installed_skr_mini_e3_v12_motors_got_louder/
I used 2.0.5.3 on my SKR Mini E3 without issues.
Have you done a M502 to load the firmware default values, followed by a M500 to store them to EEPROM and a M503 to check them? I expect this is the issue.
If that doesn't fix it; are you using up to date configuration files (link provided in the firmware download)?
If you are, and still have the problem, please try current bugfix-2.0.x to check if you are still having the problem.
Firmware:
https://github.com/MarlinFirmware/Marlin/archive/bugfix-2.0.x.zip
Configuration Files:
https://github.com/MarlinFirmware/Configurations/archive/bugfix-2.0.x.zip
My output:
M569 S1 X Y Z
M569 S1 T0 E
And check:
SENDING:M569
X driver mode: stealthChop
Y driver mode: stealthChop
Z driver mode: stealthChop
E driver mode: stealthChop
Built from Marlin bugfix-2.0.x branch. Copied over the official Bigtree configuration files, then modified them to work with the latest branch (attached).
Marlin.zip
Ran m502 then m500 then m503.
Still seeing the reverse effect of the M569 S1 Z E X Y command
I find it weird that the command is acting in reverse of what is expected. This is a brand new board just arrived a couple days ago from Amazon.
Which stepstick are you usign? TMC2209, 2208, 5130....
@Bob-the-Kuhn as I can see 51xx and 220x use reversed function for same GCONF bit 2.....M569 send S value directly to function en_pwm_mode and I can't see any override to it.
Which stepstick are you usign? TMC2209, 2208, 5130....
It's the same btt skr mini that I have, uses 2209's. I have no issues, however.
I'm assuming it's a config file issue, as @desertblade indicates he is using "official" config files as a reference. So probably outdated.
Please try again with the config files from the marlin repository :) I'll have a closer look when I'm back at my pc
Which position is the SPREAD jumper (near the X driver) on the board? Try moving it to the opposite position.
We have a winner! @thisiskeithb
Looked at this image:

My Spread Jumper (red jumper) was in the opposite location. Switched it around and M569 command is working as expected.
Figured it might have something to do with recent batches of the board.
Big thank you to everyone. Hopefully this will help a few other people.
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Most helpful comment
We have a winner! @thisiskeithb
Looked at this image:
My Spread Jumper (red jumper) was in the opposite location. Switched it around and M569 command is working as expected.
Figured it might have something to do with recent batches of the board.
Big thank you to everyone. Hopefully this will help a few other people.