isn't that what its supposed to do?
only fire up when there is flow passing through the boiler and turn off when you let go of the trigger
if the flow is not enough it will not operate the flow switch, I find if i use a small jet on my handtool it doesn't have enough flow to fire up the burner.
so might be a problem with your flow switch, if this is the case then alter it from a vertical position to a slight angle.
what exactly is happening?