If there are problems at intersections, that means that the bike lanes aren't protected enough. Amsterdam for example doesn't have these kinds of issues because their design (and especially light signaling) is better.
Unless you design the intersections properly, then you're never going to achieve that protection. The best way to design them would be to follow how limited access highways/motorways interact with surface streets. In other words, they use interchanges.
I agree. The problem is that I have never seen those sorts of lanes in the US. The choice is between semi-protected lanes which may be worse or no lanes. I don't know precisely which is better, but I usually choose to not use the protected lanes due to issues at intersections.