Not LDO, that's between Vin and Vcc.
You say 32U4, but what board is the chip on? Pro Micro, Leonardo...?
There may be a diode to protect the PC if the USB is plugged in while the Arduino is powered externally (i.e. through Vin, via the LDO). That diode is probably dropping the ~0.3V
What does your multimeter read on the 5V/Vcc pin, rather than the direct USB voltage?
a 3.3:1 potential divider.
(Vcc - 33k - A9 - 10k - GND)
That's 4.3:1, not 3.3:1. The resistors have a ratio 3.3:1, but the voltage divider they make has a ratio of Vin:Vout = (33+10):10. Are you calculating incorrectly in your code?
The internal voltage reference on atmega32U4 is 2.56V, not 1.1V as on atmega328.