This issue was addressed back in 2014 but does not seem to be solved correctly.
When debugging in visual studio a "dynamic" version of the typescript file is opened, but it is incorrect, old, has been updated. Yet the dynamic version is where the break point is hit.
I've tried "Build-Clean project". Showing the hidden files (.js and
.js.map) in solution explorer and deleting them before rebuilding which should (and does) recreate the files. Yet still for some reason a cached file remains and this is what is being used.
EDIT - workaround - Restarting Visual studio, results in the correct files loading... sometimes. Sometimes you have to restart numerous times and of course many times per day.