1) Are you running Windows? If so, are you running the DKPProfilerUploader? This is definitely the easiest way to ensure your data gets uploaded in a timely fashion.
2) If you're doing the manual upload (either you're a Mac/Linux user, or you don't trust executables), make sure you're uploading the file from WoW/WTF/Account/AccountName/RealmName/CharacterName/SavedVariables, and NOT the file from WoW/Interface/Addons/DKPProfiler