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Calibre does not support applications on devices. The folder choices are the ones given when the device was created.
You have three choices:
1) use connect-to-folder, specifying the folder you want the books to go to.
2) use the user-defined device driver, specifying the path for the books. In this case you must also disable the blackberry plugin.
3) report a bug and hope that Kovid agrees with you.
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