by default, windows explorer doesn't show hidden files. so, when you highlight all of the files you can see, you're not really highlighting all of the files that are there--that is, unless you've checked the box telling windows to "show hidden files and folders"--then something screwy's going on. in general, though, you can trust the pie chart.

EDIT: same story with maemo. the built-in file explorer doesn't show hidden files and folders. if you want to know how much free space you have, don't just "highlight-all".