Can you tell which brand of ballasts/bulbs you have installed? And this issue is not related with location of ballasts.
Well this mostly happens with no name HIDs. And another i see is because of large amount of current draw at initial startup of HIDs. Since you told us that it happens on initial startup. OEM and Branded HID ballasts pull about 10-11amps each at first few seconds of startup then it stables around 5 amps. This range is normal and does not cause any issue. But yours are 55w so it will be pulling around more than 12amps each at startup which is quite high for the wiring,electronics etc.
Now you will have to tell me that are the HIDs branded? And what happens when you turnon the HIDs while keeping RPM till 2.5-3k.? And lastly have you used a Relay Harness?
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