I have been helping out on the forums a lot recently and have had multiple instances where there are problems with peoples' code because the not block is not functioning properly. Recently, on my own game, the same thing was happening. Strangely, I tested this on a new project, and it seemed to be working.

As an example, this wasn't working in some code by @theforgottenwisp :

if <not <[c] = [0]>> then 
 tomatoes
else
delete this clone
end

but this did

if <[c] = [0]> then 
 delete this clone
else
tomatoes

Tomatoes is just placeholder text for some code that doesn't matter.

Was it some variable and did the code ever set the variable to a different value?