ffdshow devs tell me the problem is fixed in rev 3835. When that's actually released I'll give it a try.

They also suggested that ffdshow may not be the most suitable program to use in this manner.

Unfortunately, they closed the bug report so I can't reply to get specifics why they said that.

It's has me still considering rewriting to go to lossless 5.1 in this guide, but it's just a much bigger pain.

5.1 wave is an awkward format, the channel order is different from DD 5.1 so you have to re-arrange the channels, it takes an extra link in GraphStudio and an extra step to encode the final output.

If anyone following this thread has specific knowledge why ffdshow isn't a good Dolby encoder, I'd like to find out more.