Do you have the dark mode enabled system-wide? Or just in WinSCP? Does the flash occur in the dark mode only (or does it just make it more noticeable)?
I unchecked "Enable Multi-Monitor Taskbars" in DF and the flashing returned in about 60 seconds.
* System wide dark mode.
* The flash happens w/ WinSCP Light Mode, Dark mode, or Automatic mode.