Ah... trigger errors - my least favorite subject.
I would, and will only ever use a 36-1 crank trigger with an aftermarket system, first off taking the primary trigger signal from the cam is tricky because of movement caused by the cam belt (cams driven by chains are marginally better). When viewed with a timing light the difference in accuracy between crank and cam triggers is like night and day.
I base my opinion on getting management systems running on a number of Toyota 4A-GE and 3S-GTE engines.
What are the chances that the VTEC switch over causes a load on the cam belt? This has the potential to cause the primary 24 tooth trigger to be missread, which should mean the ECU stops providing a spark and injecting (beware the systems that go on a "best guess" in the event of trigger error).
Can you change the VTEC engagement to happen lower down the RPM range to see if the problem follows the switch point around?