Yes, the iso resistance varies as batt voltage/temperature/etc changes over time. Shouldn't change more than 10-15% I would expect. For more safety and redundancy Alta built in circuity into BOTH the positive and negative legs of the HV DC system. If the fault is in the negative side of the leg that's another clue. Since you disconnected the DCCP with NC in isolation I'd lean towards something in or around the battery pack. Could be water in the LV pack connector. If that's not the case and the problem seems to be pointing at the pack there's literally dozens of potential sources for a low negative iso numbers. ANY interaction (and there's many) between the LV and HV circuits inside the pack could be the cause. The HARDWARE biggies are - 300 to 12v DCDC converter and associated circuits, the negative contactor or associated circuits, any one of many opto-isolator circuits, any one of the many data line interface isolators, a few high to low Voltage regulators, the isolation measurement and monitoring components and circuity themselves. Other potential causes - Any water and/or humidity inside the pack, loose conductive debri, damaged cells and/or modules, etc. Also, any corrupt firmware files might do it as well.
Bottom line, other than making sure things are nice and dry the only thing you can do outside the pack is re-load all the firmware (which is always a good idea before digging into the hardware).