ok..
so you're starting the bike (engine running) and it's blinking on + off....
(it shouldn't blink if you turn the bike to "ON" but don't start the engine, either...)
best guess: double check your wiring for correct connections + eliminate any possibilites for potential shorts, or..
the ballast may be bad. Discharge lamps like HIDS don't "dim" when voltage gets low - it either has enough power to ignite the lamp or it doesn't. What Rhythm mentioned was correct - if your battery is low or there's some other problem with your bike's electrical system, that could cause the light to blink. If the bike is functioning normally otherwise (it starts, the hi-beam has full power, the turning signals work, etc...), I'd check the wiring first...
also - you might have pinched some wires / connectors when putting the front cowling back on.
last ditch: put the old halogen back in + connect it to the original wires (NOT THE HID BALLAST!!!) - if it works normally, I'd suspect the ballast.