Yes, provided the issues you have with Windows don't also stop you from installing themes, etc.
Though the issue causing the install to fail on Windows could just as likely happen on Linux too, depending what it actually is..
I suggest you do a filesystem check and bad blocks flagging. From windows, do "chkdsk f: /x /f /r" in a command prompt as a user with admin rights, or on Linux, do "fsck.vfat -at /dev/sda2" as root (make sure the device is not mounted).
EDIT: Perhaps try a "restore" from iTunes (this will wipe the iPod's hard drive) before the filesystem check.