VS 2012 debugging Unexpected symbol reader error while processing <file.exe>
For Visual Studio 2017, closing all open instances and restarting worked for me. I might have gotten away with closing fewer, for example instances with unrelated solutions open, but I have not tested that.
[VS 2012] Ok I got the answer that fixed this problem, so I'll post this here so that people have no such problem in the future.
A solution is to change
Debug -> (app) Properties-> Configuration Properties -> Debugging
from Auto to Mixed. The breakpoints will automatically work.
[VS 2015] Closing all instances of VS 2015 and restarting fixes the problem for a while at least. The 2012 fix does not work.