In a very rare case, the Sony STR-DH540 did not initiate playback of 5.1 and 7.1 audio formats after multiple retries in the HDMI Audio Latency tool, even though stereo audio formats played without issue. Increasing the audio latency measurement test pattern wake up time to 2 seconds resolved this issue.
This problem completely resolved itself after turning off the receiver for an hour or two.
To avoid this sort of problem, the retries could have increasingly long test pattern wake up signals.