It may be an issue with how your theme is handling the available Markdown scopes. If you're interested, check out the
Neon Color Scheme on Package Control - I wrote it to take advantage of as many scopes as possible, in as many languages as possible, and the default
Markdown.tmLanguage doesn't look too bad with it. Even if you don't like the colors I've chosen it might help you tweak your own theme more. If you have any suggestions on how I can make it better, or just have questions on theming in general, please open an issue or submit a pull request and I'll do what I can to help out.
Searching through the
.tmLanguage file has its uses, especially if you're looking for that one scope you can't seem to find but know should be there, but a much better way to go about improving your syntax highlighting theme is to use @facelessuser's
ScopeHunter plugin. I have it bound to a custom keybinding, and set up to display in a small panel at the bottom of the screen, and can find out what scopes are in effect under the cursor just by hitting a quick key sequence. Having the panel option set makes things a lot easier than using Sublime's built-in scope finder, as that only displays in the bottom bar, disappears fairly quickly, and can't be copied.