From experience... I know that just because I can swim and ride a bike (for 60+ miles) doesn't mean that I can RUN... without huffing and puffing.
When you go the longer distance... are you timing your miles (or kilometers?) and keeping the pace the same for each one?
I know for me, as I have begun upping my distance, I have really tried to focus on long and slow. When I start to breathe too heavily, I just back off the pace a little and catch my breath.
Also, do you run different distances and paces? Or is your running workout always the same? You should have some short runs with speed and then longer runs at a slower pace. From what you said below, I couldn't really tell if it's all the same or not.
Finally, it's my belief that some people's bodies are made for running... and others... have to work a little harder at it. I am one of those ones who has to work harder. But, if you keep working at it... you can get better little bit by little bit.
Good luck.
"Life is not a journey to the grave with the intention of arriving safely in a pretty and well preserved body, but rather, to skid in broadside thoroughly used-up, totally worn out, and loudly proclaiming: WOW WHAT A RIDE!!!!"