Just some random thoughts.
It sounds to me like you have more than 1 issue. One is getting your pendant working,?and the second (from what you originally said),?it sounds to me like you are ending up with missing steps which I think is a bigger issue.?That could have a number of possible causes, some of which could be mechanical, some could be electrical, others could be software.

Which any of them is can depend on how you look at it.?
Ultimately if you are skipping steps, the software is pushing the hardware faster than it can go.

That might be the software not having the capability of the system input properly in to thinks like slew rate limits cutting speed limits etc.
This is where having another software suite available could be valuable.
If you never skip steps in Mach, and only see it in the Planet CNC, well then it is the software that you want to look at]
You talk like it can be one OR the other, but not both being available to you.
.
It might be the drivers not having their current limit set properly. {Were those replaced when you had your "glitch?}

It might be your motors are under sized for your system {Unlikely unless you changed them}

It might be a mechanical issue, [is everything free of sawdust?, does the "sound" of the system change at any point when moving the full range?]?

Is the problem limited to a single axis??

Does it happen when you are not cutting anything [but air]?

If it only happens when you are cutting [More likely with any of the causes] does how often or how much you are off 0,0,0 seem to relate to how MUCH you are cutting, or how new/sharp the bit is?

?

"?I admit my logic was flawed when I thought it would be fun to learn how to use a CNC router."
Cant help you there, but your perspective may change when you are "on the other side" of solving the issue.

Jim Klessig