There is an option in the Routes configuration named something along the lines of
'show routes even when inside' (sorry, I'm not at my gaming PC at the moment so can't check the exact name for you) that I found I had to enable to get Routes, Gathermate2 and FarmHUD to work for my herbing on nUI 5.07.25 with 5.0.4. Without enabling that option the routes shown on the main map were not visible on the minimap or on the FarmHUD display. I can't say for certain but your problem sounds similar so give that a try.
