Although you see one extension, know that there are several versions of the PDF format. Not all of them are as backwards compatible as you would expect. Perhaps the website only accepts PDF format 1.6 and 1.7 and you have created pdf files with the PDF 1.5 format or lower.
Your PDF viewer/reader can handle these files, but I am not sure about the website. Like Tomos says: more info is needed for a proper answer, else your guess is as good as mine.