I have this exact model also 550EX and whether alone or in combination, I always prefer to use manual.
This flash has a high GN but then as you say, and if in F based, auto sensor mode, sensor should work accordingly and not sure why 2 stop under. Unless you have set the flash in M mode at 1/4 power (Mode>M>Select>x2 minus). Check to see if power is on 1/1. If so then I am clueless.
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