I just want to add that I had this problem often on my dualboot laptop
running Edgy and Feisty. The problem went away at some point and hasn't
been back. My system always worked fine, so used to often force a skip
of the check on my FAT32 drive(s). Not advisable though. Just thought
I'd mention that so you know you're not the only one Mathiasdm.

PS. If you reply using email please delete the quoted text before sending.
PPS. Mathiasdm, remeber you can update the original bug instead of posting the 
new results as new messages. Seems better to me than leaving out of date info 
starting the bug report.

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Boot fs-check error - Differences between boot sector and back-up
https://bugs.launchpad.net/bugs/72293
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