Background: If you have already collected a network of track and merge new elements into it, the calculation of what is already there and what is similar and can be consolidated can be very time intensive.
Workaround: The only alternative is to merge the track by hand (yellow sign) and then later recreate a route based on the spitted and joined tracks. This will also give you the opportunity to initially set up your way-point perimeters.
> QuickGuide Tutorlal
a) The GPX file you import is actually a recorded workout of your own (possibly containing heart-rate data), so it's an activity.
b) The file contains a route created by someone else and you want to add it to your own list of routes.
c) You are interested in the tracks and way-points contained in the file and you want to merge them into your network of tracks -- to be used in future routes you create.
Solution: when you import a GPX file, TrailRunner asks you if the file is to be imported as an activity or a route. Chose either option.
When you want to import the waypoints only, go to the Document Toolbar > Locations and import the file there.
Tip: For a better conceptual understanding of TrailRunner and the difference between tracks, routes and activities, take a look at the TrailRunner QuickGuide Tutorial
Background: TrailRunner is more or less two applications in one: on the one hand a route planning application managing a personal network of tracks and on the other hand a journal for your sport activities. For your better understanding, please take a look at the TrailRunner QuickGuide. The differences should be obvious after you have read it. If not, please be so kind to let me know what you do not understand so I can improve either the QuickGuide or even TrailRunner.
> QuickGuide Tutorial