philgabe:
Today, I brought my camera and flash down to the Canon Service Centre here in Singapore to check with their service rep on this problem. They were very helpful and spent quite a lot of time with me on this. They said that this was the first time any users of D30s/D60s here had complained to them about this problem.
Then they tested their own D60 and 550EX in front of me. And what do you know.... they got the same results too - the exposure with the built-in flash was OK but the 550EX consistently under-exposed by 1 stop or more. They were quite surprised with the results and promised to carry out more tests in their lab and would get back to me by next week on their findings.
Also, they confirmed that the recent firmware upgrade to 1.0.2 was not meant to address this problem and would have no effect whatsoever on flash exposures.
Meanwhile, their recommended solution would be to use the flash exposure compensation to correct for the under-exposure. Alternatively, they could reprogram my flash for me so that it would output a higher flash level to achieve the same correction.

