Flashed a Rom and lost root

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Hello Everyone,

My Nexus 7 is rooted and was running AOKP.
I decided to find another Rom to try out and downloaded one using ClockWorkMod.
I rebooted into recovery and did a full wipe, then I installed the Rom.
When I clicked reboot a message popped up but I was not able to read it entirely, it said something to the effect of "flashing this rom will overwrite........" and I didnt catch the rest.
I tried to hit "Go Back" but the N7 rebooted into the new Rom.
It was basically a stock rom so I tried to boot back into recovery and CWM was not installed.
I downloaded it from the market and could not boot into recovery.
So, I downloaded RootChecker and it said that I did not have Root Access.
I ended up having to use the N7 tool kit to re-root my N7.

My question is, how did I lose root access?
I am assuming that the rom I installed was basically a stock rom and that is how I lost root access but I am just not sure.
Have any of you experienced this?
Any thoughts on this?
Just curious.
I apologize in advance if this has already been covered somewhere else, I did search for it before I posted.

Thank you,