Here try this.. It has worked for me many times. Now i dont have any problems with losing root. It seems that when you wipe data/cache/dalvik and install a custom rom, or if you try to flash a custom rom without doing any wipe and get FC or any issues and you boot into CWM and do a wipe of any kind, this inculdes using any type of wiping program.
I know many people will say that this is not the problem, but i have tried numerous things to keep root with no luck until i did this and it works. This problem keeps popping it ugly head up every now and then (when i try to install a custom rom and have to do a wipe of anykind, but i just do what is in the above post and problem gone. What developers should do is when posting a custom rom, tell the people what version/type of root they used, and what version of busybox they are using, so that everyone can be on the same page and setting as the developers. Just my 2 cents. ( Flame On - if you want to build your post count or have nothing better to do.)