I'm using 5.5 and having no problems. You are correct that it should pick the version appropriate to the sample rate in use.
First thing to do it to go to SETUP/clock and confirm the actual sample rate. Also, look at the leds on the front panel.
If it indeed shows 44.1K you could try with the Internal Clock and see if it has the same behavior. Based on that we might get a better idea of what is happening (Monday).
