So the specific issue you've been having is caused by Vimwiki taking over the Markdown file type globally. You have a few options to prevent Vimwiki from doing that, which should help you solve your issue.
First, you could set the
g:vimwiki_global_ext variable to 0, disabling it from hooking into files anywhere with those specific extensions. You can do so by adding this to your vimrc file:
let g:vimwiki_global_ext = 0
This means temporary wikis will not be created on the fly anymore, so you'll need to use the
g:vimwiki_list variable to register the locations where you want Vimwiki to be activated. This should be straightforward if you're mainly using Vimwiki to manage a single wiki or a handful of them and you don't tend to create new ones, but rather add more contents to the ones you have.
The other option you have is to use a different set of extensions for Vimwiki that doesn't clash with the usual Markdown types. For example, you could use something like
*.vimwiki. In order to configure that, you need to set the
g:vimwiki_ext2syntax variable. You set it to a Dictionary which maps specific extensions to the Vimwiki syntax type you would like to associate with that extension. (You can use
'markdown' for the default, or
'media' for MediaWiki syntax.)
Either option should help fix the issue for you. If you don't plan to create Vimwikis on the fly, go with the former. If, on the other hand, you would like to be able to create them dynamically, but on the other hand you're fine with using a file extension different from the default ones, then go with the latter.