Here's what seems to happen with the E-Flite electric retracts.
There is a curved slot cut into the side brackets. At each end of the slot is a pocket that a brass "T" rests in at the end of travel.
To go from the pocket to the main part of the slot, the brass "T" goes over a sharp transition. This seems to be the high current portion of the travel with the electric retract gear unloaded (No wheels, just the struts.) If the gear draws too much current for too long, the protect circuits in the gear "trip". The total current draw at the transition easily exceeds the 900ma listed in the gear specs. (Even after going thru all sorts of gyrations to minimize friction, interference, etc.)
When you look at the peak current draw, it's enough to cause a four or five cell receiver pack to significantly drop in voltage output, likely to a voltage that is marginal. (Somewhere below 4.0 volts.) You also have to consider that the battery may not be fully charged, which further increases the voltage drop under significant load. If the battery pack is at 50% charge or less, the voltage drop is really significant under load!

Separate battery packs or a separate good current capable BEC seem to be in order. Additional capacitors might help lower the peak current needed from the battery or BEC.