Do you have the latest UniCode versions installed? They are working fine here with just 2 gotchas.
1 - Once you have closed the GUI, you cannot reopen it again until you have closed out the export dialogue & reopened it.
2 - Neither the DD or the DTS encoders will produce DTS-WAV or AC3-WAV. You need to go all the way back to N3 for that side to work.
3rd party stuff.
The Minnetonka is all standalone, not plugin, and is old.
For DTS, I would go for the DTS SAS or MAS encoders, as the algorithm has been much tweaked. With the MAS you also get full DTS-HD capability and the StreamPlayer which also allows you to decode any DTS stream back to PCM as well as a full preview with a quicktime if required.
For Dolby, I really do not know what to advise. The Dolby Media Toolkit is brutally overpriced, and is OSX only (Why, for the love of god, when all BluRay authoring systems are PC?). SurCode is good, but are all standalone as well - probably the only other alternative.