Don't know if it's the same problem that you're encountering, but I recently was working a project that I had started in MQX 3.8.0 on the K70 platform. I had finished the first phase of it earlier this spring, and was ready to develop the next phase. I saw that MQX 3.8.1 had been released, so I figured it made sense to upgrade my MQX installation and BSP.
Boy, was that a mistake. After diff/merging all of the BSP and PSP changes into my custom BSP, I could not for the life of me produce a functional application image. I would trace from startup, and the debugger would somehow get lost before I hit the first line of my main thread. At one point, I somehow managed to flash an image that did report to the serial port, but every I/O device creation I attempted failed. I eventually threw my hands in the air and went back to MQX 3.8.0 which I still had installed on a different workstation.
Moral of the story... if it ain't broke, don't upgrade. I'm doing a K20 project now, so I have to use 3.8.1 to get the K20 BSP support. I just hope it's not broken like my K70 project was.
Interestingly, Freescale published v1.1 of the MQX 3.8.1 installer on 20 Aug 2012. I don't know if they patched anything or just altered the installer; I'm tempted to install the previous version on a different workstation and diff them to see what changed.