Okay...here's a newbie's advice...
I don't know if what you describe is happening to you on all of the
boards you're working with, but I'll pass along some advice given to me
by the teacher who taught me.
Now before I start a flame-war, keep in mind, this guy was teaching a
class of rooks, myself included. You pros out there may have
better/different technique, and if so, please share it _politely_!!
If the board you are jointing is convex _towards_ the knives, it is
very difficult to straighten it out on a jointer. This is due to the
rocking effect that takes place. In a gross exaggeration, think of
trying to "straighten out" a rocking chair's "foot"...where along the
foot would you put the pressure in order to begin flattening it?
This would be true regardless of whether you were jointing the edge or
the face of the board.
His advice was not to bother, but instead flip the board and joint the
_concave_ side first. Then, if you're jointing the face, run the board
through the planer with the jointed side down and it would flatten the
the concave side. If you're jointing the edge, run the board through
the table saw with the jointed side against the fence...the blade will
do the rest.
Of course, the other issue with the tables/knives being co-planar and
well-aligned is also true, but look into technique as well. This has
worked well for me.
Now, again, for those of you with _fantastic_ technique, BE GENTLE IN