For starters, oil-based poly WILL bring out the grain whereas water-based poly doesn't. Is what you're seeing happening around 'knots' in the wood? If so, this is just character and you leave it alone (so to speak.)
SO as I see it, you simply sanded and tacked and SEALED the floor? This may sound 'picky' (so I need to be clear) but when you say finish, I/we know it to be the poly. There ARE clear 'stains/sealers' but it doesn't sound like you did this, right?
As for resanding and all that, yes, if you only do this in 'spots', you'll get an unevenly, finished floor. YOu need to do the ENTIRE floor w/the sander. It's all or none, otherwise, you'll see 'patchwork' in the results. Keep talking to me.