For some rider / position combinations the discomfort won't tolerably go away and you need to change your position.
From personal example, I started riding road bikes 6 years ago and it has been a good journey but the bent over position has always resulted in discomfort for me in the upper back, even though all the other roadies seem to be able to do 200 km rides in that position, after 50 km my body is aching. I am relatively underdeveloped in my upper body and have a long neck which is the major cause.
Thing is I'm very tall and I could never find a bike where I could have the handlebars level with the seat.
Anyway to cut a long story short, I have just recently (yesterday) bought a 25" hybrid (trek is the only one that make that large size) and have finally got that elusive handlebar and seat uniformity that has made riding much more enjoyable.
I still keep my road bike (a fixed gear actually) because for short fast rides its exhilirating and one day I'll find a compatible riser stem that doesn't cost the world, but to get to uni every day I will ride my much more comfortable and relaxing Trek 7.2fx.
I heartily recommend getting a second hybrid bike for your 7 mile commute. 7 miles is such a short distance that you don't need to race and if you arrive in comfort, it is much more preferable to arriving a few minutes early.