Join Date: Dec 2011
Location: Morris County, New Joisey
I'd suggest checking your outfeed table to ensure that it's at the same height as the knives. It it's a bit lower, the board will tip downward slightly at some point when it's past the knives, lifting the remaining portion of the board and possibly leaving some of it untouched as you described.
If your outfeed table isn't adjustable, you'll have to set the knives to be at the same height as the outfeed table.
And you're correct; you typically surface one face of the board on a jointer, then follow with a thickness planer to get a uniform thickness.