BaseCamp 3.0 doesn't have this issue, as far as I know. It actually renders lines more correctly than BaseCamp did in the past, which may make them less obvious in some situations, but would generally make more readable/accurate maps.
If by some situations you're including using the map to find a path then that's true. You simply can't see the paths which I think is something we're expecting to be able to do.
Here's some samples from SwissTopo v1 and v2. You need to look at the v1 version to see where the path is then you can locate it in the v2 version.