@Damaen & Draconis
This was happening to me while I was figuring out the settings to run on Vista. Make sure you set the Planetside.exe file in the SOE folder to run compatability mode with Windows 95 (odd, right), and then make sure the SOE launcher file (the one that is put on the desktop) is set to run normally, so don't edit it at all.
If you continue to get problems, uninstall and reinstall the launcher. It has to update from that webpage once, so once it's updated, you shouldn't have to go to it anymore.