Tool length, tool change & offsets: A total mess

Lately I found myself in a total mess when using linuxcnc.

It is for parts that I have been making for the last three years and I have been using linuxcnc for work since 2008.
I have no formal training in Milling.

The mess started after adding a pendant to my configuration and after trying using two different tool types, requiring a physical tool change.
The changes to my configuration were made by a fellow forumite but I am unsure if it actually about this config, it can also be a coincidence.

I'll try to give a good account of what happens.

To start, I set up the first part of the job, for tool number 3, a straight 3 mm bit. Tool set at lowest point, enter M06 T3 in MDI, then touch off tool length 0.

Enter M06 T10 in MDI for V-groove bit.
Set that at the lowest point, touch off tool lenght 0.

I then continue to touch off X and Y to get the program inside the machine limits.
Two weeks ago I used the pendant for the first time, and used that in touching off.
I noticed that when I move X with the pendant, the selected axis in "axis" does not change to X.
So If I move the X axis to touch it off, I need to make sure that before I touch off, the X axis is actually selected, otherwise I'd touch off the wrong axis.
(When I move an axis with the keyboard, the axis is automatically selected.)

Then start milling.

Now for the Mess.

Just about every time for the last 2 weeks, the live plot on screen plus the coordinates shown with it, do not match reality, or vice versa.
Today, the code was clearly within machine limits, both on screen and in reality, but I got a message that movement on axis 0 would exceed machine coordinates.

I have also had that the live plot was shown outside machine limits, with the tool above it, where it would not go to work, but the physical position was correct.

And ALWAYS, I can get the machine to the position where I park it at the end of the session by using G53 which is at the limit of X and Z.

I am at a total loss how to go about solving this and would welcome any pointers to get started.
By now I am ready to scrap my configuration and start fresh, just to get my productivity back.

You have to issue a G43 after your tool change to activate the tool offsets. Some other important offset related codes to remember,
G92.1 (cancels G92 offsets)
G49 (cancels G43 tool offsets)
G40 (cancels tool radius offset)

Thanks guys!

I'll give it a try when I'm back at the machine.

If there are any cutter diameter compensation values active, are these visible in the tool table?
I ask because there actually are values in the table at x and y for the tool numbers with which I'm having problems.

If this is the case, then it is curious how I actually engaged tool radius compensation, it was not by issuing G41 or G42.

Tool diameter is in its own separate column. The X, Y, Z,... offsets are applied as a tool lenght with the G43 command (or G43 Hn to specify a tool number other than the current tool).
Tool Diameters are applied to the left, or right of the commanded path movement by G41 or G42 (Dn to specify the tool number)