Only when you don't use the <UpdateId> and <BuildNumber> tags Plus! will look at the version number. When Plus! does look at the version number you will receive a update notification each time the installed version differs from the DB version, regardless which version number is higher. Because some coders use non-standard version numbering there is no accurate method to determine which version is newer.
When you use a <BuildNumber> Plus! will check if the <BuildNumber> in the DB is actually higher than your installed <BuildNumber>. Because <BuildNumber> must be an integer it can be compared accurately. Which is why using a <BuildNumber> tag is highly recommended for scripts and skins in the DB. See
Auto-Update for Skins & Scripts FAQ for more information.