I have currently analog mixing desk connected to my soundcard (8 analog outputs to 8 different channels) + digital SPDIF from soundcard to multi-fx box, which is also connected to mixer from its analog output.
Problem here is that I cannot use parallel compression because latency difference in DA conversion is causing phase cancellation.
Perhaps you could send an impulse/click through the whole system — i.e. through both the analog output and the spdif output — then record the final output from your mixer somehow.
Capture the recording, then take a look at it in the sample editor. There should be two distinct impulses with some amount of delay in between them — one from the analog out, and one from the spdif out. It may be a few milliseconds, or it may only be a few samples.
Once you know the precise amount of delay, you could then artificially add some extra latency to the output which is arriving at the mixer too early, in order to correctly re-align the signals. In Renoise, you can do this by setting the track delay to some amount in milliseconds, or if you need more precise control you might consider using something like Voxengo Sound Delay.
Voxengo also has “Latency Delay” plugin, so I only needed that on SPDIF send channel instead of “Sound Delay” on every channel. http://www.voxengo.com/product/latencydelay/
I guess Plugin Delay Compensation has to be turned on for “Latency Delay” to work.