[j.p.s]

Did you run fsck on the kindle or your PC? Running it on a mounted partition is a bad idea anytime, and it is my understanding that, at least in the case of a kindle, what shows up over usbfs is not the real partition.

[root@kindle root]# grep mmc /etc/fstab
/dev/mmcblk0p1    /             ext3   suid,exec,auto,nouser,async,rw,noatime,nodiratime 0      1
/dev/mmcblk1p1    /mnt/base-mmc vfat   defaults,noatime,nodiratime,utf8,noexec,shortname=mixed              0      0
fsp#/mnt/base-mmc /mnt/mmc      fuse   rw,max_write=65536,max_readahead=65536,noatime,exec,nosuid,nodev,nonempty     0      0
[root@kindle root]# grep mnt/us /etc/fstab
fsp#/mnt/base-us  /mnt/us       fuse   allow_other,umask=0,uid=0,gid=0,rw,max_write=65536,max_readahead=65536,noatime,noexec,nosuid,nodev,nonempty     0      0

/dev/mmcblk1p1 is the OS partition
/dev/mmcblk1p1 is the user store partition

Note the presence of the 2 fuse file systems.

If /dev/mmcblk1p1 is corrupted I guess you could disable usbfs by enabling usbnetworking and ssh in and unmount /mnt/us and /mnt/mmc and /mnt/base-mmc
then run fsck on /dev/mmcblk1p1

I have no idea how to run fsck on a fuse system.