hard drive partitions problem

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http://askubuntu.com – Hi im fairly new to linux, please dont be too hard on me. Im using Ubuntu 11.10 in a wubi instalation. As im using clementine tu listen to music i have in my partitions, each time i power ubuntu up clementine loses the librarys and has to rescan the partition all over again. a similar thing happens to Transmission bitTorrent client... each time i shutdown the computer and power it up again it loses the location of the files if they are in one of the partitions.... Is there a way to fix this problem? Is it normal? Thank you in advanced. (HowTos)