Hey Stuart,
Sorry for the slightly delayed response, but I have a similar problem also with the line tool default layer changing randomly in AC11. Mine keeps changing to the layer the grid is on, (which I have also locked to prevent them from moving, which make it doubly annoying!)
And you're right, the trigger is simply switching to the fill tool, and then back again.
I'm guessing it might be related to the AC10 origin of the stripped down file that I used to start this file. If I start a clean new AC11 file using the default AC template, the line layer works fine.
I've noticed there are also a couple of other features that don't quite work properly either which are possibly related, but I haven't bothered to try to sort them.
So, no solution to the problem from me, but least you know you are not alone!