...but the error persisted...
What error?
To be clear, syntax highlighting of code blocks is **NOT** part of "standard" Markdown. If you get it added to the [CommonMark specification](https://spec.commonmark.org/), that is, by working with the [CommonMark group](http://commonmark.org/) and convincing them to make it a standard feature, once it's in the standard and implemented, it will just work in the Geany Markdown plugin. Until then, installing patches or extra packages won't help.