I was Luckily able to find a jupgrade version of my backup site before this sidebar position issue was a noticeable problem. It could, I guess still be the VM update that is causing this but I'm not 100% if that was in my case because as I stated before I have a version where the VM upgrade was not installed yet but was still having this SideBar/footer issue. I will try again to recreate it with a fresh install of this template on my demo server once I have my website all setup.
All I know from this point forward I will never be one to quickly do a vm update to my site unless tested completely on my test site first. I've only wasted HOURS of my time downloading and uploading different versions of my site...having a 102MB site and slow internet is not a fun combination of doing this with.
I guess it beats paying $100 for support in which case I was very close to spending to get this resolved.
I do hope for rest of you...there is something resolved with this. From what I can see...for whatever reason the Category/Product/Checkout page styles are not pulling from what the other template pages are and pulling from the vmsite-ltr.css which I do not see the case on the quickstart template...there are also other variable of CSS sheets these pages are pulling from. I'm not sure if that helps but thought I'd point that out. Good Luck!