Currently APT doesn't support Gigapixel images because in the way it is done now, we need to lock the whole picture into memory (related to RAM) to export. So it depends too much on your configuration. Anyway, the picture won't be exported to its full resolution (limited to 200MPixels). But if you check http://www.autopano.net/forum/t8277-apt-beta-dev-plan , you'll see this is our main development those days. So expect more very soon.
Right now, if you really want gigapixel and are not afraid of krpano comand line tools, there still is some tools on his website to tile pictures. Here is a possible (and not personally tested) solution: 1/export a low def version of your panorama 2/do your visit with APT and this low def, export 3/tile the Gigapixel image with krpano tools (http://www.krpano.com/tools/) 4/replace the pano node in the APT generated XMl by the one provided by krpano Hotspot placement should not be as precise as you wish (due to low def workspace), but this may provide a good working base for some beautiful gigapixel visit.
I ended re sizing the images to half their original dimensions... and output worked! I then resized to 90% of the original dimensions and it worked... Not sure why the problem occurred, but its working now