Can you please tell us what file extension the executable you used had
and while filesystem is on you usb drive? There was a change in the
default mount options for vfat that restricts executable permissions to
windows executable files for the windows FAT file system a while ago:

udisks (1.0.1-2) unstable; urgency=low

  * Add 00git-vfat-showexec.patch: Enable the "showexec" vfat mount option, to
    avoid data files being executable (which causes confusing question dialogs
    in nautilus which only have one sensible answer). Patch taken from
    upstream git head. (LP: #14335)

** Changed in: ubuntu
       Status: New => Incomplete

** Tags added: maverick

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Could not able to run the executable from the USB flash drive only in Ubuntu 
10.10
https://bugs.launchpad.net/bugs/663815
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