Usually the problem you describe is caused by a disconnect in how you have the safety/retract height set and how you are setting your zero relative to the stock.
If you’d post the G-Code for a small project which exhibits this error and step-by-step notes on how you are securing your stock and setting zero relative it we’ll do our best to work through this with you.
On the gripping hand, what sort of joints are you trying to do?
We’ve worked out a number of different joints here:
If there’s some sort of joint you wish to do which you can’t find files for, please let us know and we’ll do our best to work through them with you — I’ve also done some alternative joints such as the relieved finger joints shown at: Design into 3D: Boxes: Magazine storage (I’ve got an improved version I’m working on for that which uses a radiused endmill to eliminate the visible void), and I’m also working on a blind miter with hidden spline which doesn’t require a the vertical fixture either.