From what you have described it appears your version of paperscan is outdated. Please make sure you are using the 3.0.59 edition. To update it you can either click on "check for updates" under the general tab or uninstall it completely and download it once again from http://paperscan.orpalis.com/. On the current version you can choose where to save your scanned files after you click on the "save" option under the "general" section.
If you have any further questions do not hesitate to ask.
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