Thank you for the reply jmjf. Appreciated.
I understand all you said, I've had problems with this Bootstrap theme during updates before (the Bootstrap menus stopped working after WP 3.5 update for example and several users had to point out the issue. That Boostrap update just before the holidays at the end of December was supposed to fix, but I still don't like how the menus work on Bootstrap) so my confidence in the Bootstrap theme is not great.
And right when I started using Bootstrap something got completely corrupted on my previous install of the Bootstrap theme (media library got all messed up, pictures were not showing properly. No one had any solutions to fix on the forum) and I could not fix, so I had to re-build the entire site from scratch. I decided to give Bootstrap one more chance, but vowed any more problems with the theme and it was probably better use of my time to move to another theme (for example, I don't see the frequency of updates on Bootstrap come by that I see on other themes. Can't understand why that is). Things were going OK on my site for two months since the full re-build (second install of Bootstrap) until this last week.
I don't need to uninstall all the plugins as a week ago everything on my site was perfect. I notice it's always the offered solution to uninstall every plugin for some reason on these forums. But in this case I can't see what un-installing all the plugins that worked fine a week ago will get me for the time spent. The only thing that I know that has changed in the last week or so is WP had a release to 3.5.1 and a couple of plugins had updates.
Now two plugins I've noticed short-code issues on. The 1 existing plugin that was working fine for months I noticed earlier this week started giving problems and not showing the short-code form properly.
The only reason I installed the Easy Digital Downloads was to see if the same issue short code issue happened and sure enough it did. Which leads me to deduce it's either a Bootstrap theme issue and/or WP 3.5.1 issue or a combination of Bootstrap and WP 3.5.1 impacting my short codes.
I'll wait and see if any other solutions come by to get the short-codes working again on my site. If I have to un-install all the plugins to get the short codes to work, I'm just going to go all the way and move to another theme and do everything once so I hopefully don't have to encounter a major problem every few months. I have an old site that I have for years on the Suffusion theme and I never had an issue with it. Everything always just worked or if there was an issue, it was a simple configuration issue I could figure out on my own. On this site I just wanted to use a "responsive" theme as I know many people use smartphones and tablets. But now I'm second guessing that decision to go with these newer themes as they seem to have some issues.
I have notes into the the two makers of the plugins (the two plugins that I've noticed the short code issues) on their support forums to let them know the short codes on my site are not working and that I'm using WP 3.5.1 and the Bootstrap theme. Hopefully they can offer some fixes.
Thanks for the help. Appreciated.