Yes, the multiple font sizes will mess it up. The text scaling, transform, ect is very complex in the backend in Photoshop where it stores that data.
If after making a new text layer it messes up still then we can do a screen share on Monday. There is too much to explain in a post how to test and troubleshoot so a screen share would be what we need to do.
Just make sure to not scale the new layer when sizing it to fit the template. Type in the size manually in the tool bar until you get it where you want it. If you scale it to make it the size you want then Photoshop stores the original size, plus a scaling factor in the date hidden to the user. That is where I have seen bugs in Photoshop. However, even when scaling, I have only seen this affect when using the pop up window for text testing.
Anyway, let me know if it works and if not then we can do a screen share on Monday