Upgrading MC server removes horses from "old" parts of map

Horses occur in only a particular area of the map, a "new" area, a long way from the "old" spawn area (10 minutes train ride (real-time)). Horses are brought back, and corralled within the walls of a building.

Whenever the server is updated (last two times) any horses currently in the "old" area disappear, however horses in the "new" area persist.
Other animals (at least chickens & pigs) do not disappear.

If the server is stopped and re-started, everything is preserved as expected. It is only on an upgrade this happens.

This happened both on the upgrade to 1.7.7 and 1.7.8.

It seriously curtailed my kids' horse breeding programmes.