> We have a MCF52254-based board connected to a tablet OTG port
The MCF52254 also supports OTG mode. So in your use, which end is acting as the Host and which end is the Peripheral?
If the MCF52254 is acting as the Host, can you plug a keyboard, mouse or Memory Stick into it? Do these work when it is "locked up"?
If the MCF52254 is acting as the Peripheral, can you get any sense out of it from a Computer?
> What registers or bits should I try to perform a hardware shut down of the USB peripheral?
It doesn't seem to have a "reset everything" control bit. I'd suggest writing all the writeable registers (out of the 43 or so there) back to the "Default Values" listed in the Reference manual, making sure you disable all interrupts.
The MQX Driver may be keeping some "internal state" that means it can't be initialized a second time. I don't know anything about MQX. I'd suggest reading the sources.
I'd suggest you search these forums for "USB" or "OTG", especially in the MQX "place":
https://community.freescale.com/message/435935#435935
Tom