I'm not sure what could be causing a system-level lockup. Indigo always logs error messages to the system log -- there is no option to enable/disable this. This type of lockup is normally caused by either a corrupt system, bad memory, or some type of hardware failure.
Technically, it should be very difficult for Indigo to cause such a failure, but I'm sure it is possible.
I'd start by running the Indigo Server with no interface (PowerLinc) hardware connected at all to see if it still hangs. It won't be able to control your HA obviously, but this will help rule out a faulty PowerLinc (or USB cable) as the culprit.
If it still crashes, then I'd turn off the Indigo Server to see if the crashing continues.
That should help us track down the problem -- is it the PowerLinc, Indigo Server, or something else.
Oh, one last thought -- you are not running Indigo 1.8 at the same time at all, are you? I could see bad things happening if they both accessed the PowerLinc at the same time...