The question is way too general to be able to give a proper answer, especially without any details on how it won't work and what kind of app it is.
I can say that I've run multiple .NET apps on various machines which ran LV programs (including some that interacted with LV) without a problem. I don't expect that LV should have any general collisions with .NET.
That said, there may be specific issues which are impossible to predict based on your info. For example, maybe the LV program you're running uses a resource (such as a TCP port) which the .NET program wants?
The best way of figuring out what's going on is probably to have the .NET application properly report what errors it's running into and working from there. If it can't report, you should try stepping through it or removing parts of it until it starts working.
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