In v1.6.7, setting up a route manually at the continent level (e.g., Outland) routes and waypoint data are not shown at any map level other than that continent.

For example, a route connecting Black Temple in Shadowmoon Valley through to Tempest Keep in Netherstorm does not show a line cutting across the Hellfire Peninsula zone map. Also, including a waypoint for Magtheridon's Lair in Hellfire Peninsula will not show anything either. Looking at an overview of Outland, though, does show the route.

Note that the route does appear on the minimap while flying through the Twisting Nether (the interstitial area which has no zone map of its own), but the line disappears when entering a "proper" zone that has its own map (like netherstorm, et al.)

Commenting to say this is still an issue, exactly as described here.