make sure you have the map config like:
map: {'jquery/jquery': 'jquery'}
otherwise, it should be possible to see what the different modules
names for jquery are. What I would do is put a debugger in
SystemJS's fetch ... you'll see some code using XMLHttpRequest
object. There you could see what module name is making an ajax
request for 'jquery.js'.
I can explain more, but not until Monday. Maybe matthew will be
able to help you out if you have any further questions.