I noticed, in the communities I'm subscribed to that if you click on the top left of the stackexchange community pull down menu, that it lists the questions of the community and when you click on 'Questions' in that community you get different questions. Is there a difference in the two in the sorting of questions?
If you're talking about clicking the site logo, or going to a site by clicking their name in the Stack Exchange dropdown, then that action will by default, take you to the 'active' tab (or, as @Cai said, the tab you last chose on that site):
This shows the questions that have been recently active, which includes edits, new questions and 'bumps' by community, in order of their activity (newest activity first).
Note: On Stack Overflow, if you have the new-nav enabled, it will take you to the 'home' tab by default instead.
Clicking the 'Questions' tab will by default take you to the 'newest' tab (or, again, the last tab you chose on that site):
This only shows questions in the order that they have been asked (newest first).