Introduced in XOOPS 2.3.3 (but not noted best I could tell) is a new system template system_homepage.html. Whatever is in this template will display on the home page in your content area.

My content container was displaying on the home page when it hadn't before (since there wasn't content). After a review of the code, I found a hidden DIV tag (display:none inline style) with the p content of "Change the content of this template to fit your needs.", so did a code search and found the template. I have an if statement in my themes (as do most of the programmatic themes like Morphogenesis based themes) where the content container only shows if there is content. Because this template displays by default, the content area was showing on my home pages, but because there was no (displayable) content it looked out of place as well as rendered incorrectly.

I emptied the template and that "fixed" it. If you'd like to place content on your home page in the content area (smarty tag of xoops_content), then put whatever you want in this template, and it will display your content container, etc. Of course, you will have to define some smarty constants in a language file somewhere (if using Morphogenesis, the theme.php is likely a good place) so you can translate to other languages you use.

Since I couldn't find anything on this, I've posted here in case others run into this issue. Good luck!