There have been several reports on the EFS-Web listserv that EFS-Web is puking on its own PDF forms. The chief trouble area is the Application Data Sheet form. The user carefully creates a computer-readable ADS and uploads it to EFS-Web. EFS-Web then pukes on the form, stating (falsely) that it is not really a PDF file.
The workaround is to print the ADS to PDF using CutePDF. Then that PDF file can be uploaded to EFS-Web. EFS-Web will gripe that it is not an official USPTO form but will at least permit the e-filing task to be completed.
In the old days I would have characterized this as a Big Problem because in the old days, EFS-Web actually auto-loaded the bibliogaphic data into Palm (and from there into PAIR). But (as I blogged here) USPTO has been gradually chipping away at this and now almost none of the bib data gets auto-loaded. So you might just as well upload a CutePDF version into EFS-Web.