Boost Converter Efficiency goes down as Duty Cycle goes up?
The main power losses in a boost converter can be summarized as follows:


Power switch switching losses (e.g. MOSFET, BJT. Hereafter I will refer to the Power switch as the MOSFET)
MOSFET conduction losses.
DIODE switching losses.
DIODE conduction losses.
Other conduction losses (e.g. inductor resistance)


The efficiency of a converter is given by:
eff = Po/Pin = (Pin - Plosses)/Pin.

As the losses change the efficiency therefore changes.

One can not make a blanket statement as to why the efficiency reduces or losses increase as the duty cycle increases because then one would need to know all five loss parameters as a function of current, voltage and switching frequency.

However, a simplified explanation of this phenomena is that the MOSFET conduction losses are unequal to the diode conduction losses. As the duty cycle increases, the MOSFET will conduct for a longer period and the diode for a shorter period. This in turn alters the power losses in the circuit. If the DIODE happens to have higher conduction losses than the MOSFET for example, then as the duty cycle changes, causing the DIODE to conduct for a relatively longer period than the MOSFET, then the efficiency will decrease. This is a simplified explanation, but the main principle is that as you change the duty cycle, the operating conditions for each element in the circuit change. Since the losses for each device depend on it's specific operating point, then changing the duty cycle changes the losses.