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I think you are limiting virtual memory per process for a user, when you want to limit physical ram total (across processes) for that user.
If you use virtual memory as a limit on physical ram, you can't set the limit with any accuracy. Some processes might use as much physical ram as they use virtual memory, so a higher limit on virtual would let them use more physical than you want. Other processes (as you seem to have discovered already) use a small fraction physical ram for a large amount of virtual. Stopping them from doing so stops them from running at all, even if running them unlimited would have used very little physical ram.
Pre user across multiple processes is also hard to do. The relevant limits are per process for the specified user.
If I knew the solution, I would tell you. I'm posting to explain that the place you are looking for the solution is further from a real solution than it might appear.