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Are you talking about inline HTML in your markdown that is intended to be markup (and is displayed as text instead), or is intended to be displayed as text (and is displayed as encoded text instead)?

Once you differentiate between the three possibilities you can make sure you’re applying htmlentities in the right spot. Beyond that, you might look at the $double_encode parameter for htmlentities and make sure you’re not encoding things twice.

Let me know when you want to see code

In general, you should automatically be sharing enough code to make your issue clear. When you know generally where the issue lies, all the more reason.