Okay, I'd admit at the start I have been away for a while, but I don't understand why somethings are no longer working in the latest version of Iclone.

I have a puppet that I set transform points for on the timeline (traveling from point A to point B).
I set an initial start motion (standing up looking at cellphone).
I tested the animation and the puppet moved from point A to point B just as planned.
I then opened Motion Puppet to give it a walking animation.
I masked out the parts I used in the initial motion and previewed the cool walk motion. I noticed the puppet did the cool walk motion but wasn't moving forward.
I assume (my bad) that this was just an added feature and went ahead and recorded the motion. 
The first time the character still didn't move. After some unsuccessful online research, I decided to first do the cool walk motion, then added the transform points.
The puppet is now either stopping short by at least a quarter of the way or going way past the stopping point I set.
It's like on this new timeline, any motion I add comes with its own (unseen) transform point.

Thanks for any assistance.

Is the curve on your transform keys set to linear?

There are some very significant changes in the way keys are applied in the timeline with version 7. Th keys are finally included within the motions when you use the motion editor. Much easier to work with that way. 

But you are probably seeing a change when you are adding keys in a clip, and then the next clip does not have them, and so jumps a bit. You can copy the keys between clips if you need to, or just set them in the new clip to something close. Another option is to merge the clips and then add keys to effect the longer merged clip.

Have a look at these videos:

Thanks,
I actually went back and watch these videos a few time more.
My solution turned (what works for me anyway) is the sampling process. 
I was able to see all the keys and manipulate the ones needed.