Which programs do you know that conflicts with NWN's?
I came across by one recently. It was an AVG browser extension. I must have downloaded it when I went for AVG anti-virus after my computer crashed.
Since removing all traces of AVG and using the free editions of Avast and MalwareBytes instead I have no longer had this problem.
I had a problem with RegCure Pro as well. Once the membership expired, and I decided not to renew, it got upset and corrupted both MalwareBytes and NWN, forcing a complete reload, and destroying all my characters that I had created over too many game hours I care to admit. However, this turned out to be a good thing, since CEP would not work on the previous installation, but does now.