So I installed Ndure 3.0 successfully to my Xbox but was wondering if there was a fix to something. Whenever I start the Xbox now it either goes to the time set every time or goes to my Xbox live setup and I can't exit that. I know you just have to press the four buttons to get to the main screen but is there a way to avoid this completely?

Yes. Install the softmod properly.

As it's already (badly) softmodded the easiest way is to use HeXEn (Google Heimdall's Xbox Engineering Disc) to update to Kingroach NDURE 3.1 or Krayzie 1.1.1.