In version 2.20:
If I refresh a geocache (using gc4l), each refresh creates a new "set" of associated waypoints for this cache. So after e.g. five refreshs, I have five "parking location" associated with that cache.
solved http://help.locusmap.eu/responses/refreshing-reloading-of-a-geocache-increase-the-number-of-waypoints
Update:
It seems like this does not happen with every cache. Refreshing some caches works without duplicating waypoints, refreshing some others not...
This one is an example for this behaviour: GC2T5CH.
I'm pretty sure this didn't happen in V2.19, and of course I didn't change any settings in Locus... ;)
Update 2:
Didn't see menions answer before posting this... Good to see it's already solved. 8)