This can be a bit of a pain with some software and and the typical solution is to create a component that is nothing more than copper attaching the grounds. I had an engineer that created such a part, and placed the copper joining all the grounds on a new layer. This was a great idea, but after he left the company the next engineer didn't know that the Gerber files needed to have that extra layer included. That was a darn expensive mistake.
From a design standpoint, separating anlog, digital, and different power supply gnd/returns is vital to the integrity of the circuit and isolation from noise. Measuring voltage on a 12V line requires you connect the scope-probe ground to the 12V return, likewise the 5V and 24V busses. If the designer isolated those lines, there is good reason to believe they should stay isolated. I can't argue with your success, but I'd guess that the problems you were trying to fix still exist and will evidence themselves in degraded performance and/or damaged components.
Cliff, this is an interesting situation. The engineer was trying to keep track of the different grounds, but the software didn't know that. What he did made sense, but then again, so did what the software did.
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