Comment 84 for bug 1104476

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Alexey Brodkin (alexey-brodkin) wrote : Re: Network manager cannot connect to WPA2/PEAP/MSCHAPv2 network without CA_Certificate

Disagree. In my case (fresh & updated 13.04 64-bit) I don't see configuration file changes on reboot.
I may expect it to be modified if you remove your current Wi-Fi connections from known ones in NetworkManager and then will try to connect to it again - this indeed will create a new config file in "/etc/NetworkManager/system-connections/" that will have "system-ca-certs=true".