I suspect your 1065 programming loaded only the 4 control channel frequencies but in EZ Scan you loaded (the default?) all site frequencies.
EZ Scan has an option to import/load only the control channel frequencies - and, IF the information posted is accurate, the control channel frequencies are all you really need.
However, if the information is wrong and/or changes (without notice), installing a subset of site frequencies could result in you hearing nothing from that site (that would be all or nothing - all talkgroups).