Not a problem! I'm glad you're asking the questions here, on the forum--so that other people can learn from your experience with the tool!
So--how are you lining up the handibot on your material? By that I mean--how do you know where you're expecting the pocket to be cut? If you set the handibot up for a cut and send the bit to the bottom, left-hand corner of your pocket...(you can find this by examining the vector in VCarve--if you click the "move" function and choose "absolute" and select the corner as your datum--the current position will be the location of that bottom left hand corner...or you can just hover over the corner and the rough location will be displayed at the bottom of the window)...so when you send the bit to this bottom, left-hand corner location--is it going where you expect? Is it already off by that 1/4" you're seeing after you cut?
If so--then you can fix that offset by:
1. Moving the handibot itself (difficult to do perfectly)
2. Moving the home location of the handibot (quick to do--but then your cut area is reduced)
3. Moving the vector that you're pocketing in VCarve (left or right, up or down by 1/4"...this might be the easiest to do)
Make sense? For example--I was doing some wood inlay for a Christmas gift last week--one of the inlays cracked after I had take the material out of the tool. So I set the machine up again on the wood--homed the tool--then manually move it until the cutter was aligned with a corner of the inlay. I went into VCarve and moved my shape around until that same corner was in the exact same spot in my design--toolpathed it, and recut the pocket for the inlay and repaired it. That was a lot easier than trying to move the material around to match my existing cut file.
Brian