Widgets Disappear and Reappear | Footer Editor "Site-Link" Not Working

Good afternoon all, First, let me start by saying that I very much enjoy this theme; it is by far the best one I have used (hence why I purchased the pro version). I have the theme installed on two different sites with the exact same layout. However, on one site, in the customizer, when looking at the homepage, I am missing: - Primary Sidebar - Optional Post Sidebar - Optional Page Sidebar However, when I click on a post, the Optional Post Sidebar reappears in the customizer. When go back to homepage (in customizer) the option again disappears. To edit the Optional Page Sidebar, I have to click on the page in the customizer window and then on the left, where the customizer is, the Optional Page Sidebar reappears. This is a bit of a hassle and further, on my other site, I don't have to do this; everything appears, no matter where I go on the site (while in appearance --> customizer), in the Widget Options. Both sites have the exact same layout. The only thing different is the content. Could this be a faulty install? Wordpress Support said it might be b/c wordpress itself is working fine. Lastly, the site link short code in Appearance --> Customizer --> Theme Options --> Footer Editor is not working. The site link [site-link] is entered correctly in footer editor but does not appear on live site. The only thing I see is a period. Please help!