I'm assuming that QlikView Desktop and QlikView Server are the same version (for example, 11.00.11282). If this is the case, then the most likely reason is that you developed using a very different screen resolution with Desktop, and you are viewing the files in AccessPoint with the Ajax client, The Ajax client, as opposted to the Plugin client, cannot autozoom, unless you increase or decrease the zoom factor of the entire page.
There is a button in the toolbar of QlikView, as well as in the View menu that is very useful when you aim to Ajax users, that is "Turn on/of Webview". Webview is the closest approach to what the users will see using an Ajax client in your Desktop. Use it when developing or install the IE Plugin in your clients.
Hope that helps.
I've started using the "Turn on/off Webview" button; however in that view am I right in thinking that I can't make changes the biggest issue I currently have is that I have a container with seven reports/charts and in webview bar the first word you can't see the rest of the title. Is there anyway to make these tab widths widers?