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 absolutely real truth to improper sous vide cooking and botulism. Clostridium botulinum is an anaerobic organism - it grows when there isn't oxygen - like in sous vide vacuums and canned goods.
The risk is that sous vide cooks both without oxygen and at temperatures so close to the perfect repoduction rate for the organism. If you cook it a little lower than recommended, you could be creating a perfect place to reproduce. Clostridium botulinum dies around 126 F (52.222 C) - so most sous vide won't go lower than 130 F (54.444 C).
The opponents state that the temperatures in general are far too low and if we were cooking for a few seconds, it would be. Luckily, pasteurization is a function of temperature and time. This is part of the sous vide magic. Bacterial death is a result of heat and time - if you have a high heat you may only need it for seconds. If you have lower, but sufficient heat, then as long as you cook it long enough (see recommended reading below) - then you can still pasteurize the food. Sous vide often cooks foods for hours and hours - either for taste and/or pasteurization sake.
A great resource for information here is Douglas Baldwin .
Additional, real, danger comes from if you store your finished product in the vacuum bag at improper temperatures (not freezing). Botulism spores need to reach 250 F (121.111 C) to die (this is why, in canning, some food needs to be pressure canned). You won't hit that in sous vide cooking. If you cook the food, cool it, and then store it in a non freezing temp - there's a real risk that the spores could eventually become active and reproduce. If you're going to keep sous vide food after its been cooked, generally freeze it and then reheat (quickly, in sous vide terms) in an eating temp sous vide bath to consume.
Best Answer
There is no real safety issue if you do a really good job removing ALL of the air with the displacement method. The challenge is in removing all of the air. According to J. Kenji Lopez Alt at Serious Eats, "Excess air causes oxidation that can develop into off flavors or promote spoilage."
The second issue is with the seal if the Ziploc bags. Generally speaking, these bags are not designed to withstand high temperatures, especially not for long periods of time. It is quite possible the seal will fail during a long cook, ruing your food.
You could certainly use Ziploc bags and give it a shot, there is no dooming reason not to try it. Before cooking your expensive brisket or whatever you're looking to do a long cook with, I recommend trying to overcome these two issues with something cheap to see if you can get rid of all the air and if the seal will last.