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This may be related to the latest version of the initrd tools. Since I installed the most recent release I get errors mounting not sda partitions, where Debian resides, but hda (NTFS and FAT32) and hdb (Debian).
Moreover Linux reports that the hdb partitions are ext2 (they are ext3), gibbers about running fsck and drops me into a maintainance shell.
I just press Ctrl-D and when KDE is up I can access alll the partitions.
I assume that this is a bug which will soon be fixed. There seem to be some problems floating around at the moment. I am in dependency hell but assume that all will ultimately be resolved.
I'm having the same issue in Ubuntu - I use unison regularly to sync the home directories on 2 serial ata drives. The problem began happening after I accessed the first drive from the second drive using different versions of Ubuntu (5.04 vs 5.10) I ran fsck with a full scan and detected no errors but it still gives me the boot up fsck error and when I exit the maintenance terminal, the the system boots and runs with no problems.