It seems to be even more complex. To try an eliminate a interrupt firing unexpectedly. I modified the code to the following:
__disable_irq();
LPUART_WriteBlocking(LPUART0, command_str, i);
__enable_irq();
where disable disable_irq() & enable_irq() use the assembler command cpsid and cpsie respectively. And there still appears to be unexpected pauses when transmitting over the lpuart i.e.
