Help - Ext HDD Referenced Master Files Gets Connected to Wrong Drive

I just bought Aperture and upgraded to 1.5 and am a new user. Prior to the external/open library, I would not have bought Aperture because I need to access my images on both Macs and PCs.
I spent all day yesterday creating project structure, albums and importing images into Aperture. This morning when I launched Aperture, the referenced masters on external HD were somehow now connected to my Boot Camp WindowsXP partition. When this occurred, I did not have my external drive connected.
Naturally, I connected the external drive and relaunched Aperture but all the images were referenced to my XP partition with directory path that belongs to my external HD (i.e., path is XP/Photo Lib/2006/..., instead of what it should be LACIE/photo Lib/2006/...) I was able to reconnect by selecting one image and reconnecting all function. Easy enough but troublesome.
Has anyone else experienced something like this? Is this a bug on 1.5? Am I doing something wrong - I could not find any setting that would cause this behavior.
I am using MBP so this is bit of a big deal for me....
Thanks in advance.
  Mac OS X (10.4.7)   XP Pro

My comment was too generalized - sorry.
Actually, the version file I was referring to is a version that gets created when an external editor is used. As you know, Aperture can create either TIF or PDS file to be used by an external editor. Once it is saved in the external editor, the preview is updated and the version is stored in Aperture Library. Unless I save the file using "Save As" into a different location manually, the edited file is in Aperture Lib. I will have to export the file into the directory of choice.
If Aperture saved the external edited file into where the master file is located, then Photoshop'd or any other editor modified files can be accessed directly without having to go through the extra steps

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