Never ask me again work only for positive answer for the main question (Overwrite?). It is ignored if you press any other answer. Due to bug when you press Newer only it considers it as possitive answer and makes it overwrite all files. I'll fix that. But anyway, once you press Newer only it is applied to all other files, you may not need to check Never ask me again.
The Windows version does not save when I check "Don't ask me next time" when it challenges me to overwrite an existing file unless I select "Yes". I don't want to select "Yes"; I want to select "only newer" so that (as expected) only those files that are newer than the remote files will be uploaded and overwritten. Five times in a row I selected "Do not ask me again" and clicked "only newer" (or newer only, whichever it is). It never saved honored my request to never ask me again. As soon as I clicked "yes" as a test, it suddenly honored my request.
This is regarding version 3.7.4 for Windows.