Son of a. I'll have to give this some thought. You may not like my answer. Please back up both internal and external sdcards FULLY.
Already on it. factory reset incoming by the sounds of it eh!
also just to note I was working on getting a swap partition going, was about to install the init.d support scripts and found this issue.
I do not believe I messed up the /sdcard/ as it works just hunky dory. I did all the partition creation on the external SDcard in my netbook.
Only commands issued were the likes of fdisk -l for listings of the partitions and mounting just the swap partition. I did not touch any other partition so this should not be a result of that work.
I do have a mirror of my sdcard-ext as a class 4 device so not worried about that. and data is backup don't care about installing apps again.
Thanks