Nominal voltages can vary a lot from actual, and both batteries and diodes show this tendency strongly.
The 1.5V nominal voltage on a dry cell is for a fresh cell that's not being asked to deliver much current. Ask for more current, and you'll get less voltage out of the cell. 45mA is a lot to ask from a 9V battery, so it's undoubtedly delivering less.
Similarly, the 2V drop across a diode will vary with the individual diode characteristics and with temperature.
The rule of thumb for dry cells is that you haven't gotten all the energy out of them until they're running at around 1V to 0.9V per cell -- that works out to designing your circuit to work with a battery voltage from 9V down to 6V, or even 5.4V. That, in turn, means that you should design for two LEDs in series, with an appropriate current-limiting resistor -- and expect that your intensity will drop considerably from a fresh battery down to a dead one.