I dont have many explicit delays but there is enough code to have the same effect.
I might have found my bug. It seems that sleep in PHP only works off whole numbers.
So sleep(0.5) was actually sleep(0).
Doing some more testing seems to indicate that the serial buffer was being filled hence unpredictable values being executing.
A delay of 100ms seems to be fine. I'll run it for a hour to be sure the buffer isnt slowly filling.
The only reason why it would fill is if its taking longer to send the data to the LCD than the delay from the sending program.