This is something of a complex question, but to be short: I think the sous-vide cook before marinading is denaturing too many proteins up front, and the intense marinade is just damaging those further.
What you're doing in the first step could be considered a form of brining: using salt to season the meat, and to denature some proteins in an attempt to get the meat to retain more water later. By sealing the bag, you've done this without adding any additional water, which is fine. You're also cooking it at the same time, denaturing further proteins.
The only problem is that acidic marinades also denature proteins, so when you add the acidic marinade, you're repeating that action yet again and breaking them down even further. It's not entirely surprising that by the end of this process, your meat has broken down so much that the texture is unpalatable.
My suggestion is to back off. In a sense, this does work "better" than a traditional marinade, but it's working too well. Reduce the amount of acid and salt that you're using. You can do this by quite a lot because the flavors will pair with one another and strengthen both in the finished dish. Additionally, I see no reason to separate these steps. If your goal is to season using the salt and add flavor using the marinade, do that at the same time, during the sous-vide step. Keeping them separate does nothing more than add time and complexity. It's the overall amount of action on the meat proteins, not the order of events.
EDIT: After thinking on this a bit further, I realized that something else was probably going on too. Cooking the meat sous vide with salt is also a little bit like braising: the combination of temperature, moisture and salt is breaking down and dissolving some of the connective tissues and collagen too (also a lot like making stock). So that's even more you're doing to your poor meat. I think my original conclusion stands but I would add a further caveat that you probably shouldn't even attempt this for relatively tender cuts (like beef tenderloin) as it's just too much. Maybe a tougher cut with a lot of connective tissue could stand up to all this treatment, but it's a lot to ask..