Strange problem when copying files

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Hi.

I've just had the following strange problem. (using kernel 2.6.18.1)
On a FAT32 partition I copied a directory with some big files (about 1,5GB at all) with cp -a .
Afterwards i diffed the results (diff -q -r) and one file was different!!! I copied again,... this time another file was different.
I looked at my logs but they didn't show any suspicious errors (like harddisk or memory issues).

I rebooted,.. tried again,.. an than it worked.

I've fsck'ed the partition but no errors have been reportet.

Any ideas what's the reason for this issue?
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