Thank you for your message. I did try /public_html/store/ previously but the update was then also showing 'Unable to locate CS-Cart software'.... But actually I kept at /store and it seemed the update could find the software but I was still receiving the error.
But I finally updated the store!

At the very bottom of all the errors there was a continue button. Nervously ignoring all the errors I hit continue, more errors appeared but I hit the continue again...not it went to finally update screen. Clicked continue and it updated the store as normal!
So I am still not sure why i was getting all the errors but I am updated now.
On a bit different topic, is anyone using Searchanise? I did some checking on the forums at a lot of people are against it?? I did install it and it seems to work well but is this a security risk using it?
Thank you again.
-Tim