I just tried all possible combinations and it looks like suEXEC daemon is the problem.
When I have suEXEC daemon on, either with LVE or CageFS, I have this 2-3 second hanging between page loads. Page loading is super fast -when it starts- the problem is that it seems like it's hanging, waiting for a little bit, and then the page comes instantly.
When running either LVE or CageFS mode, and Run on startup = Yes, the "hanging" problem is gone.
It's not a *huge* deal, and maybe some will think it's ok, but for me knowing how my sites loaded two days ago, and seeing the difference when changing to suEXEC daemon, it's noticeable.
I'm changing my settings to not use suEXEC daemon for now, and maybe have a look at it Monday morning. Have a nice weekend all!