Hi Jaap,
I think I understand what you are doing.  You have a stop trigger configured and you want to stop your acquisition in phase with a given output value of the board.  It also appears that the stop trigger lag is such that the board doesn't receive the trigger before it outputs the next word.
Here are a couple things to note.  The DIO Clear does not reset the output lines.  The lines will keep the state of the last data output.  Also, there is no way to speed up the trigger.  I have a couple of suggestions to help though:
1) Can you trigger 1 sample before you need to?  I was thinking you can trigger on the falling edge instead of the rising edge before the sample you need (or invert the trigger condition).  If you can give me more details on your 
trigger condition I might be able to help with suggestions on this.
2) You can set up your stop trigger with some post trigger samples to be output.  This means, when you receive your trigger, you can still output 2 or more samples (but not 1 sample).  The way you do this...
In NI-DAQ function calls, you can configure amount of post trigger data in DIG_Trigger_Config, and the amount of pre-trigger data = total buffer size - number of post trigger points.
In LabVIEW, you may configure the number of pre-trigger data in Digital Buffer Control.vi and the number of post trigger data = # of updates - # pre-trigger updates.  This means you would configure a buffer of 1000 and pre-trigger of 997 and you should be able to get your 3 extra data points to finish with a zero.
Anyway, I hope that helps you out.  Have a good day.
Ron