If you are measuring flow through a heat exchanger, forget the cabin pressure. The relevant criterion is pressure difference before/after the heat exchanger.
The Magnehelic gauges are very reliable. If you can gently blow on a port and get a needle deflection, it's a 90 per cent certainty the gauge is fine. Best to trust the measuring tool - I've often found I've disbelieved measurements too... but they've been correct.
It's not unusual for heat exchangers to be doing little (eg in my measured experience, the standard intercooler on Peugeot 405 diesel).
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