I have been playing around in the tracker and what I did was have one voice start in the first channel, second channel blank for several rows, then introduce a new voice in the second channel. Third channel is blank for still longer and then introduces a third voice.

I find with the third channel in play sometimes the playback of the channels becomes out of sync. Is there something I need to do to make each channel play at the same speed? My expectation was that blank rows would occupy the same amount of time as a row containing a note, but perhaps this assumption was incorrect?

Hmm...I just tried this again and it did not happen. Bug? Unfortunately I have no idea what I may have done to have caused this behavior in the first place.

I realized this was simply due to changing the tempo of a given channel of music AS a sound effect. When the pattern is played back, it uses the tempo of the given sound effect. So if your pattern has more than one channel, and one of those channels has a different tempo, they'll get out of sync. I.e. clearly not a bug, this is by design. So typically when writing music one will have the same tempo specified across all channels. In fact I found the relevant manual language:

"When a pattern has SFXes with different speeds, the pattern finishes playing when the left-most non-looping channel has finished playing. This can be used to set up time signatures that don't divide into 32, or double-time drum beats etc."