Hi,
I have the same problem. I have been talking with Freescale and the problem is when it is switching from bootloader that uses internal to the programcode that uses the external code. Fresscale said that one can reprogram the cpu with a bootloader that uses the external clock then it would not change clock and it would solve the problem.
I have not tested it because it meens that I must reprogram the bootloader on all chips I sell. And that would take to much time. It can the be better to write a own reflash function.
//Bertil