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Which version of SmartSection are you using. I use 2.12 RC1 on my site and pdf files upload just fine.
Is it just pdf files or do you have problems with uploading any files to SmartSection?
In the admin section of SS, what is the maximum filesize that you've specified - is it a big enough number?
In admin section for SS, is "[PERMISSIONS] User submissions?" set to "Yes"? If yes, have you given your user group permission to submit?
Can you upload other files to other modules? I had a problem with the server that my site is hosted on where the .tmp file didn't have the "write" permissions.