You are probably uploading the Previews. You set the size and quality of the Previews (they are always JPGs) in Aperture prefs.
Aperture is extremely efficient with computer resources. One of the results of that, is that files of your Versions don't exist until you create them by exporting. (What you see as full-size files in Aperture are created on-the-fly, and are not saved.) "Export" means "make me files according to these parameters I set". There are no full-size files of Versions to share with other programs until you create them by exporting Versions.
Either the plug-in must create them (it appears the one you are using does not), or you must. There is no getting around it. Create an Image Export Preset with the settings you want, create the files you wish to upload by exporting Versions from Aperture using a selected Preset, and then select those files with the uploader.