We always book under separate records. and have had this happen several times. I think they look at the seating charts and figure that people who aren't on same res are traveling solo and won't mind (or notice?) the switch. It irks me to no end, as I often have to work hard to wrangle 4 or more seats somewhat together, esp in F, and by the time we notice changes, we are separated all over with nowhere left to go. I know that sometimes the switches are made for FAMs (and try to avoid booking "FAM rows" as best I can), but I have also boarded often to see families seated together in our previous seats.
Robin