when "soft-takeover" option is checked (as it is needed when using one MIDI CC for more diffrent parameters depending on its focus) then both "Enable only when effect configuration is focused" and "Enable only when effect configuration is visible" options are not saved and thus not working correctly.
It is not new as it was already reported in the other thread somewhere in March 2019, but I experiece it now with Reaper v6.29rc4, 32bit & Windows10 x64. It got me today when I was trying my arduino DIY built "one knob" micro MIDI controller
More posts in this thread, please read:
MIDI learn is not remembering settings
https://forums.cockos.com/showthread.php?t=218623
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EDIT 20210919: This bug has been fixed in v6.36+dev0916 version.