Whenever this has happened to me, it's been in cases where I had an error in my ascx/aspx file. Typically, I'll forget a closing </portal> or </panel> tag somewhere. When that happens, the feature is excluded from the page, and it can be difficult to troubleshoot (as you're finding). I'm actually not sure exactly where (or even whether) you can find an error for that condition. So when a new custom feature is not being included on a page, I go back through my form and look for mismatched tags. Fixing those has solved this every time for me.
I hope that helps.
Jamie