DOH!!!
I found it. Single stepped into each task as it started and my USB task was the one that was causing the issue. I had just enabled that task last week after sorting out the code to programme the USB host controller.
In here I was using the following to setup the IO ports for the UART. I am using the eTPU for this.
J2[TXD4].function(UART_TX_ETPU);
J2[RXD4].function(UART_RX_ETPU);
J2[TXD4].hiz();
J2[RXD4].hiz();
I goofed here as the defines for TXD4 and RXD4 are defined as eTPU channel numbers and this call to J2[TXD4] was changing the IO pin state. TXD4 was defined as 4 which is the UART0 TX line.
I don't actually need to do this it seems as the call to eTPUFDUartOpen does this for me.
Thanks for all your help folks. Sometimes having a second eye on things helps to track it down.
All is back working again.
Dave...