I have a similar problem and contacted support about it just now...
Copying and pasting syntax highlighted code from various sources used to work. Now, when I do the same on the Mac (Version 6.11), it just copies with the default text, no highlighting.
Not only that, but I have now looked at my old notes, which had syntax highlighted code snippets, and they all look like this now:
This should be a solid black box of highlighted code, using a monospaced font. The other notes are even worse.
I managed to add some highlighted code to Evernote Web, which worked as expected