I am pretty sure it's something I have done, but for the life of me I don't know what.

In one of my news posts a youtube link showed as a video no issues, then a couple of posts later in a new post a youtube link did not show as a video.

Here is a link with the youtube not showing, about 1/2 down the page. https://www.crazylag.com/news/view/gaming/jack-black-launches

And here is a link to another article where youtube shows as it should. https://www.crazylag.com/news/view/gaming/12-massive-upcoming

Any ideas?

Nevermind, silly me.
I didn't have Convert XHTML to Comcode enabled in the Feature options .

Right. If you want to keep that option off, just wrap a Comcode media tag around the link.