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To be able to share data on the diagnostics and master bus, the IQAN master modules must run the exact same version of the project file. The modules check this by looking at the Project checksum. 
If the project checksum doesn't match, you will have an error about System mismatch. 

Any time you make a change in IQANdesign, the Project checksum is updated. 

Looks like the issue is that the Paccar truck requires the TSC1 to be sent with Control purpose set to PTO Governor.

The built-in TSC1 channel have these bits set to all ones, "temporary powertrain control" (the use the original TSC1).

It would probably be nice with another property to set control purpose on the built in TSC1 channel.

I think IQANdesign has always worked like this, at least going back to version 2.x. 

When you first change the scope of a channels to Function Group Output, this new FGO will be added to the bottom of the list of function group outputs. 

When you later change calculation order within the function group, the list of function group outputs are sorted in calculation order. 

I had a look at it, and I think there is a problem with how gradients are handled on vertical lines. When the gradient direction is set to default, the MD4 will draw the gradient along the x-axis of the vertical line. 

But even when manually setting the gradient to another direction, I still didn't get it to work on a vertical line control. 

The error could possibly be related to overcrowded CAN buses, with the MD4 failing to get its messages out. 

As it happened after a software update, I wonder if there are other modules on the Diagnostics bus? I am guessing here, but maybe some other module stacked up a lot of outgoing messages while the IQAN system was updating, and then when the IQAN-MD4 started up it it was way too busy on the buses..Hard to know. 

It doesn't look like J1939, it looks like 11 bit identifiers, and all the ID:s look like the CANopen defaults. 

IQANanalyze, switch decoder from J1939 to either Generic or CANopen. 

The text based file compare works on .idex files from 6.02

You can also see the Machine ID of the clone by right clicking on the file in Windows explorer, select Properties and look at the File info.