hairy_hen said:

If there is a Dynamic Range Compression setting in the encoder, I'd recommend disabling it,

I think this is what the "Compression Preset: None" is for.

However, I'm not sure about the 90 degree phase shift setting. This probably also is intended for optimal downmixing, but I don't know what effect if any it has on normal 5.1 playback.

You need to leave the 90° phase shift enabled - this is to ensure that the 5.1 can be downmixed into 2-channel Dolby Surround.

I have the Dolby Digital Professional Encoding Guidelines, a PDF downloaded from Dolby Lab's website, which has useful information and good explanations for this stuff.

I would also recommend you disable the three filters in the pre-processing tab. They are designed to make the source easier to compress and, in theory, they shouldn't have any audible effect. However your source has already been compressed to AC3 once, and I don't think that running it through these filters again will have any benefit.