Cryogen seems to have a problem generating tables from markdown. The table html tags are created, but they have no content inside them. Is this a known issue or am I missing something?

That sounds like an issue in markdown-clj to me. If I were you I'd try using markdown-clj directly and see if you get the correct table output from your input markdown. https://github.com/yogthos/markdown-clj

In general one of the things I'd like to improve with cryogen is the ability to use a different markdown engine. At this point it's doubtful that I will ever get around to it, but it's somewhere on the list of my rainy day activities.