flypadre

Why not put the loop in another loop that checks to see if the plugin is present. If the plugin is present then run that, else run the main loop.

Well, took your advice Robey and upgraded WP to 3.9 on my vps and that did the trick. The only reason I didn’t before was that it was so simple to install from the repo, however that as you pointed out was giving me a very dated version of WP. Anyway after the upgrade I uploaded my theme and it installed.

Thanks for the help all, really appreciated!

@robey I am using the wordpress 3.3.1 version because that was the version that is in the ubuntu 12.04 repository. Do you think that the version differences is what is causing my problems? I’m using Easy Phpdevserver to develop on.
@eric I developed a theme from scratch Eric, so yes I was doing work on style.css but I was also doing work on everything else as well. Everything works on my localhost running 3.8, just not working on 3.3. So, not sure that we are experiencing the same problem. Once I get this figured out, I will post what I did here.

UPDATE
I was able to get a different theme going by downloading it to my computer from www.remarpro.com and then cp it to my themes directory.
So there seems to be an issue with the way things are handled when the themes are downloaded from within wordpress.