Custom kernel SuperBlock error Please Help!!

Hello,
I have Arch linux installed on a virtual machine for a class project where we are required to hack the kernel. I have successfully modified the linux kernel 2.6.28 code, compiled and booted with the custom kernel. This morning I made the last final changes to the code, recompiled, but when I boot I am greeted with:
The superblock could not be read or does not describe a correct ext2
filesystem.  If the device is valid and it really contains an ext2
filesystem (and not swap or ufs or something else), then the superblock
is corrupt, and you might try running e2fsck with an alternate superblock:
The Arch kernel boots fine however. There were no errors during kernel compilation. Any thoughts/suggestions.

Thanks for the reply, yes this is after grub and no it is not ext2, it is ext3. I ran into this problem on another virtual machine after several kernel builds so I did a fresh install of Arch and the kernel build (along with booting the new kernel) was fine.
Note this:
The last time I compiled my kernel (virtual machine 1) I did rm -rf * on /usr/src, copied my kernel stuff into /usr/src and did the compile got the ext2 error, however, the Arch kernel was fine.
On the second virtual machine, I was in a major hurry so I copied my kernel stuff into /usr/src compiled, everything was fine. Went back into the code, made some changes recompiled got the ext2 error the Arch kernel again was fine.
I realized on these last two builds, I didn't create the symlinks 
# ln -s /usr/src/linux-2.6.28 /usr/src/linux
# ln -s /usr/src/linux-2.6.28 /usr/src/linux-2.6
Could this mistake be the cause??

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