Are both pages using the same skin?
I would copy one of the newer skins from /Data/Skins into /Data/Sites/[SiteID]/skins and then set one of those as the skin for the page and see if that makes the script errors go away or makes the file uploader work. Try a few different skins and see if any of them fix the problem, that would narrow it down to a problem with a skin.
Also if you are using .NET 3.5 I would look into updating to .NET 4 or 4.5 and the .NET 4 package of mojoPortal and also make sure that the server has all of the windows updates applied.
Also when upgrading mojoPortal always make sure you use the new Web.config and transfer any customizations such as machinekey from the old one to the new one.