I never had a copy of Filemaker 6, but do have a copy of Filemaker 5.5 still installed. Given your description, this sounds like this part of filemaker is the same for both versions. Under document preferences, there's an option labled "store compatible graphics". For cross platform compatibility this option needs to be selected on your windows platform. If memory serves me correct, you may need to extract the images from the file, take them to the windows machine and re-insert them. This is not a task that's easy to automate, but it can be done.
Your other option would be upgrade to a newer version of filemaker.
Thanks Phil, I'll try that as soon as I can get hold of a mac and see if that works.
How would I extract images from the file? I've tried to select images before but in the container there's only the option to add something over them, and IIRC export doesn't allow you to export container fields.
In later versions you can export the field contents to a file. In fact, downloading a free trial copy of Filemaker 10, converting a copy of your file and then using this feature it export the images might be you're best way to extract the images. With your version, the only method I'm aware of is to copy the images to the clipboard and paste them into another application where you can save them as a Jpeg or other graphic format file.
Before you do that though, check to see if simply changing the preferences to store compatible graphics fixes the problem without having to do this. I'm going by memory here and might not be remembering accurately.