There are a couple of different "custom templates" that are used here. One type I'm not familiar with and the other I use from time to time.
1) The custom templates I'm not familiar with are the templates that are truly custom. If you created a template using a web site or app and then submit it here, that I am not familiar with. I have never done that and I'm not sure about how that works here. I've heard many users tell me that "GIMP" is a good template builder. How these original templates do on here, not so sure. I guess it just depends on the template.
2) The "custom" templates I am more familiar with here are those I get from Google searches.I just search photos on Google and when I see one I like I save it to my computer and put it on here. I like doing that from time to time because it gives me more ideas than just the usual Bad Luck Brian and Grumpy Cat type memes.
The only problem I see with these templates is that it takes longer to feature. That can be a problem since the longer they take to feature, the further back on the "latest" pages they start out on.
I know that if your images aren't getting featured, it might have something to do with the site you got them from. Do they have any watermarks, or are they from sites that conflict with IMGflip? That could be an issue. If you just Google search, most of those are okay, but from time to time I get a few that won't feature because they have a watermark or the site that owns the picture's logo on it that I didn't catch.
If you have problems getting these to feature and they definitely don't break any of the rules, then I would check the sites I retrieved the images from. Outside of that, I wouldn't know what else to tell you. I get frustrated sometimes, too. The best way I can see getting around an image that doesn't get featured is to "share" the image on someone else's meme that is on the front page. But be sure to ask them if it's okay, just out of courtesy. I get some extra upvotes and views out of that, which makes my point total go up a little more than it would have if I hadn't done that.