Thank you Josh for your response. I found the issue! Very basic, I needed to position the router to the saved X and Y position; then lower the router to the new Z and save a new zero point.
I use a Melin 1.5" cutting depth and is 4" OAL. I seat the long bit all the way up in the router and then pull it back down about 1/4". The long bits tend to exacerbate run out. If you put long bits in the router and it sounds funny when the router starts pause/stop and reset the bit. I have a Dewalt 611 router and am usually doing 3/4" material and I do not have to raise my router any to cut the project. I also have a 3/4" spoilboard so you may only need to increase the retract height to avoid any clamps. So likely no need to move your router with a longer bit. The Dewalt has a longer body than the Makita/C3d router so I can cut deeper than the Makita/C3d router. Sounds like you fixed your problem but keep the bit seating in mind if you use a long bit in the future. I think the Z-Plus does not plunge as far down as far as my HDZ. Early Z-Plus users complained about the depth of cut not being as low as their Z Belt ability to plunge. I think they changed the configuration to allow the Z-Plus to plunge farther down without hitting the mechanical limit of the Z-Plus.
The bit must be less than .5" above the BitZero to avoid a probe failure. If the bit is more than .5" above the BitZero you will likely have a probe failure because there is a limit on the number of steps the Z will travel to touch the BitZero and you get a probe failure.