Normally, a Maketurn program sends a BaseBuildShip command (53) whenever the build order on a starbase changes. Some Winplan versions, however, send the command if (and only if) a build order is present, no matter whether it changed; they do not send any command when the player cancels the build order.
PHost includes a workaround for this bug: whenever it detects a registered Winplan client, and there is no BaseBuildShip command for a starbase, PHost assumes that the ship build order on that starbase was canceled and cancels it in the host files, too (with HOST, these Winplan versions can not cancel build orders at all).
Your maketurn must therefore, if it generates Winplan-style turn files, send a BaseBuildShip command for every active build order to keep it active and prevent PHost from canceling it. The best solution which works with every existent host is to send a BaseBuildShip for every active order, and for every changed (or canceled) order.