When I jog to the waist board with a tool I cannot get the Z-Axe to come all the way to touch the waist board.
Which machine do you have?
Which Z-axis?
Which spindle?
What length tool are you using?
How high/low have you mounted your spindle?
Post a photo?
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If you have a Z-Plus some people have reported that the anti backlash nut has come loose. That is located at the top of the Z-Plus.
Make sure you have sent the configuration. You connect but do not initialize. Then go to settings and the second tab opens. Uncheck the BitSetter, you will set that up later. Then go to the first tab and select your machine and Z. The Leadscrew refers to the Z-Plus and Ballscrew refers to the HDZ. The standard Z axis is the Z-Plus. Be sure to send the configuration and get confirmation. Then try to initialize. If it initializes you can insert a bit and see if you can jog down to the spoilboard.
Some short bits like the #102 and others can barely reach the spoilboard. So when you insert the bit you need to measure your collet length and only insert the bit so it goes to the top of the collet and no deeper for short bits. This will give you the best grip on a bit and also reach the spoilboard. If you insert short bits too deeply you may not reach the spoilboard.
For longer bits the bit should reach the top of the collet and can be inserted further is required. However never push a bit all the way up until it cannot go any further. There are two reasons. When you tighten the bit it is forced up slightly by the spring action of the collet forcing the bit in the inclined plane inside the router shaft. The second reason is the top of the router shaft may be machined roughly and can cause your bit to be out of round.
The collet on the Makita and the C3D routers are two pieces. The collet and the collet nut. When you tighten the collet nut use two wrenches. You can use the stop button to get the bit tight enough to not fall out but tighten with two wrenches. When you loosen the collet nut the collet will spring open and the bit will fall out at a certain point. If the bit does not fall out then lightly tap the collet nut and the bit will fall out when the collet nut is loose enough. It is best to have something soft for the bit to fall into like a plastic tray. You dont want your bits to fall and hit the floor.
The router shaft, collet and collet nut should be cleaned periodically and be left dry. Do not lube the collet nut and collet or the router shaft. The whole thing should be dust free and dry with no lube. Lubrication can make your bit come loose.
The way the Makita/C3D collet and collet nut work is the collet has cuts in it. The inside of the router shaft is an inclined plane that gets smaller as it goes up. When you insert a bit into the collet and tighten the nut it is squeezing the collet and it closes up and moves slightly up the inclined plane to grip the bit by squeezing the collet tighter. So when you loosen the collet nut the collet expands as it comes back down the inclined plane and the bit comes loose and falls out.
You won’t cut into your waistboard!!! 
I do a good mix of cutting down low near the wasteboard, and up higher on parts in a vise, or just taller part. To avoid constantly moving my spindle I just clamp down another piece of MDF or something to get the part up higher.
But the simple answer is, “Move your spindle down” 
(If you can.)
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I put a second wasteboard on the machine and then the work piece above that. I was having the same issue and this worked beautifully. The nice thing about this is it keeps your original washboard pristine. However, I do not have t tracks or anything nifty. I usually screw/glue my piece to the spoil board.
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I did purposely cut into my waste board 90 degree positioning square so I can load my project in the same place each time I use my CNC.
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Working on those points. In the interim I turned on the machine this evening put a quarter inch bit three flute initialize the machine and I was able to jog right to the top of the waist board! Go figure.
On the 30th of Apr I was cutting a box from Cut Rocket and my machine missed the first two passes. I was just test my skills with .5 Birch ply.
Looking into your suggestions. “The anti backlash nut has come loose” mine is secure but, down between the spindle hdz and where it mounts to the frame is a bi loose.
I would not know how to get to it to tighten it because I have no builder manual schematics.
Great you’re making progress!
If you continue to have difficulties, check in w/ us at support@carbide3d.com
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