I have no idea why that is happening. However, as a workaround, try changing the trigger or try using a script to detect if those groups are dead.
As one idea, try doing the following steps:
1. Put the following code in the initialization field of one group's leader:
squad1 = group this.
2. Delete the current trigger that detects of that group is dead, and create a new one.
3. In the trigger's Condition field, put the following code:
"alive _x" count (units squad1) < 1
4. In the trigger's On Activation field, put whatever code you had in the original trigger.
5. Repeat steps 1-4 for the second group, but use squad2 for the group's name.
See if that solves the problem.