Flavor – Does fat as opposed to oil distribute flavour better

Sous vide not only keeps the proteins (main component) at a lower temperature, but also the spices/oils/flavorings. Heat helps release the taste and aroma of all the ingredients, and the sous vide might not be hot enough to do that.

So, while it kind of kills the simplicity, you could always sautee the seasonings in oil before adding them to the sous vide bag (not until cooler though). Or just keep them separate and recombine for serving. Sous vide itself (not the vacuum part) is mainly for maintaining/achieving a controlled internal temperature, and skilled cooks don't only sous vide a dish; they might sous vide and then finish under a broiler for texture, or with a torch. If the sauce isn't working inside the bag, make it work outside the bag.

Alternately, put the ingredients in the bag the day before, and let them marinate overnight in the fridge. The vacuum action is essentially just a speeded up marinade, so this should do the same.

Also, make sure you're using enough (but not too much) SALT.

Finally, call the Sous Vide Supreme company. They know their product's capabilities and limitations and might have some good recommendations.

Just my guesses.

There is no chemical difference between adding salt early or late in the cooking process. However, if you salt just before eating, you can take advantage of textural differences between different types of salt. (Kosher salt is flakier and so gives a burst of saltiness that is quite pleasant.) (Some people will say that you should salt earlier to bring out flavors more, but once the salt is dissolved in solution, the chemical effect is the same.)

In general, fresh herbs tend to be added later in the preparation -- with the exception of parsley or dill added to soup early on to flavor the broth. However, if the herbs are added early, they must be removed, since they will lose all their flavor. (The broth will gain flavor, but the herbs will be exhausted.) You'll maintain the bright flavor if you add them late.

Dried herbs tend to react better to longer cooking, with bay leaves in particular requiring lots of time to render out their flavor.

As far as pepper goes, there's a fantastic answer to this question that goes into the chemistry of the volatile compounds in the spice. In general, I find that I prefer adding pepper later in the cooking process.

Garlic, ginger, onions, and other aromatics can be cooked a long time, although the flavor of alliums will change enormously as you cook them. (Garlic, in particular, will change enormously from a sharp flavor when raw or quickly cooked to a rich sweetness when cooked a long time.)