We currently have five of these scanners deployed on Windows 7 machines. All installations were experiencing a random error of "PDF file creation failed."
The error did not not usually occur if only a single document was scanned and saved. However, If two documents are scanned and saved back to back, this error was likely to occur at the start of the second document. Internet searches yielded nothing, but after contacting Fujitsu support, we came to a solution.
The error stems from the fact that ScanSnap Manager defaults to saving scans into the My Pictures folder. At our offices all users have their My Documents folders redirected via Group Policy to a network share. Apparently ScanSnap is sensitive to any delay when it attempts to write the scanned PDF files to disk.
The solution is to change the scan path to something other than a network share.
Right click the ScanSnap icon and select the Scan Button Settings... option.
Then, if necessary, expand the window to show all the options for each setting. Then go to the Save tab and change the Image Saving folder to something other than a network share.
That quickly resolved the errors we were receiving.