Here is some breakdown of what your original file showed.
Quickkey 0 is assigned to FRS, GMRS, MURS and a couple CB channels in your Common channels section.
Group quick keys 1-4 (only relevant to SYSTEM quick key 0) break down the FRS, GMRS, MURS and the CB channels into their own groups.
Most of those freqs in your SD North County section are not in use. There is NO quickkey assigned, so these channels will always be scanned unless you manually lock them out.
In your SanDiegoCity800M section everything looks OK except you have more Trunk freqs programmed than necessary but that is not really important. You must be out of range of this system because again, you have no quick key assigned and this system should/would scan if it were in range unless you manually locked out the freqs.
The USDefense Dept system looks as if it would trunk if the correct freqs were entered (they may be correct, I did not check)
As Dan suggested, you had close call on, turn it off.
The only thing you could have turned on or off in this configuration would have been the Common Channels on quick key 0.
Please familiarize yourself with
http://marksscanners.com/396xt/396xt.shtml for more understanding of the hierarchy of this stuff.