That makes sense. Which-key doesn’t allow the timeout to take place after gc since it knows about gcc. While that functionality is useful when you don’t know which key to press next, in situations like these it would create problems. I think your best solution would still be to modify the mappings. Maybe remap gc to gcl (comment last) or something like that.
Next time, try enabling display of whitespace characters through
set list
. If I remember correctly, they can help distinguish between the Windows carriage return character and Linux end of line character.This may help for a quick overview.