Never happened to me. I agree with lordpwn, it's probably the repair trying to delete a few parts of the data file in order for them to be redownloaded.
If you can, try to get a copy of you C:\Program Files\Guild Wars\ folder on a DVD, and update it once in a while. This way, instead of going through a repair, you overwrite your gw.dat file and simply get the new updates since the time of burning it.
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