I'm also building an isolated DC/DC-Converter.
In a completely different power-class, but the priciples are the same.
The biggest problem I'm having is the efficiency.
Through experimentation and by using this tool
http://www.dicks-website.eu/coilcalculator/index.html, I realized that the output-winding is as cruicial as the input-winding.
Using too many output-windings causes efficiency to drop dramatically.
Looking at your schematic however, the problem most likely is in the diodes. If a transistor is off, there should be VIN * 2 across it - Transformer with center tap distributes voltages like this: GND - VIN - VIN * 2.
The voltage-spike can be removed by an RC-Snubber and/or by putting the diode in series with a small (1nF or less) capacitor.
Another question: How did you wind the transformer? I managed to screw that up myself.
Best result so far: Using two wires of equal length, solder them together and add a "tap"-wire to the place where they are soldered together, then wind the cable around the core as one large continuous coil.