You could try a Tam Valley Startup Module. I had this on one of my layouts and it cured the problem.
TurnOn Module - Soft Start Circuit For Large Inrush Currents of Sound Decoders and Stay Alive Decoders
If you have a lot of sound decoders and decoders with stay alive circuits on the track, they can confuse the booster* when it starts up in to thinking there is a short because of the sudden current draw of all the capacitors. This circuit prevents that problem by putting a small resistance in to the circuit to slow the current rush and once the voltage gets up a 10 Amp relay bypasses the resistor so that there is a straight connection to the booster*. (If you have no idea what the previous explanation is about and you are not having any touble with starting your layout then you don't need the TurnOn.)
*or Command Station