Mick,
The problem you describe is the perennial one suffered by bowl turners. The rough patches you describe are, as you correctly surmised, caused by the end grain. This problem is highly dependent on what wood you are turning. Generally the harder woods are less of a problem. The ones I always have problems with are Yew and Spalted Beech.
There are a couple of ways around it. It pays to freshly sharpen your gouge before taking the finishing cut, and make this cut as fine as possible. Sometimes a light cut with a freshly ground scraper can work, but sometimes it makes the problem worse - again it depends on the species of wood.
As Jaymar says, using sanding sealer before sanding can help, or even using it before taking the finishing cuts can help as well (works well for Spalted Beech this one).
At the end of the day, a lot of it is down to practice. As your turning technique improves (make sure that bevel is rubbing all the time), you will find that this problem gradually becomes less of an issue.
Regards
Gary