Not only. I was mainly thinking about Realistic Needs and Diseases, Economics of Skyrim and Subliminal Traps (this one is not necessary by any means, but I'm very demanding when it comes to traps and stealth in general).
Alright, here's what you should do: first make sure that all your mods are up to date. Then start turning them off, half at a time, and check if a new character is able to enter Whiterun (don't do it on an old save, you'll only mess it up). As you narrow down the list of acitve mods, you may be able to determine which one is the culprit.
