It sounds like you're getting into orbit, aligning planes, etc. correctly, but let's be sure of that. I'm assuming that since you apparently haven't rendezvoused with anything yet, you're probably trying to get to ISS or Mir with their orbits unaltered from the standard Orbiter distribution. Both these craft are in low Earth orbit and have nearly circular orbits. If you're trying to do something other than this, I'd suggest putting that plan aside until you've at least done a few rendezvouses with one of Orbiter's "built-in" satellites.
When you try your rendezvous maneuver, you should be starting from an orbit where you're in a good position to do it. That means you should be at the same radius (or within a few km) of your target, and your orbital plane should be the same (or as close as possible) to your target. Specifically:
1) In Orbit MFD, your craft should show your periapse and apoapse radii (PeR and ApR) as being within a few km of each other, and close to your target's PeR and ApR values.
2) In Sync Orbit MFD, the relative inclination between your craft and your target (Rinc) should be very low, as close to zero as possible. If it's anything under over one degree, align your orbital plane to your target before going further.
You won't have to do this later on, but for the moment I want to be sure you're reading the right data off the MFDs in #1 and #2 above, so ... to double check those things, also look at values in Orbit MFD for your craft versus your target for these parameters -- SMa, Ecc, Inc, LAN, T, and Vel. These should *all* be close to being the same between you and your target, and all of them should fall into line automatically when you've put yourself into a good orbit from which to do your rendezvous maneuver. There will be small differences, but that's fine. If *any* of those show a dramatic difference between you and your target, something's wrong.
When you're at this point, just before you're going to sync orbits, do a quicksave then post the scenario file here (you'll find it in <Orbiter root directory>\Scenarios\Quicksave), and let us know which vessels are your spacecraft and your target. That would be helpful.
As others have said, turn off non-spherical gravity in the Launchpad. But be aware that there are two big things that cause an Earth satellite's orbit to fluctuate. One is that the Earth isn't a perfect sphere, but is somewhat fatter at the equator than the poles. The second is gravity from the Sun and Moon pulling the orbit in various directions ("perturbing" it). Turning off non-spherical gravity only turns off the first of these effects. It helps a lot, but don't expect your target to be *exactly* where you predict it will be for your rendezvous.
One thing that can be frustrating when using Sync Orbit MFD is that the moment you start doing your burn, the periapse and apoapse of your orbit change. There are two ways to rendezvous -- do a retro burn to make your orbital period shorter, so that you get to the same point faster than before; useful if your target is ahead of you and you need to catch up to it. Because you're in low earth orbit, you don't have a lot of room to reduce your periapse distance, so that method is really only useful if your target is *slightly* ahead of you. So I'm assuming that you're doing the other method, doing a prograde burn to make your orbital period longer, and by doing that allowing your target to catch up to you. So, from a circular orbit, just before you do your burn you might be 40 degrees past your periapse (true anomaly, "TrA" on Orbit MFD) ... but the moment you start burning, your apoapse increases and the point you're at right now becomes the new periapse ... which means that "Ship periapse," "Ship apoapse," and "Manual axis" all change to different references on Sync Orbit MFD. The way I usually handle this is to use "Manual axis" to choose my burn point, but switch to "Ship periapse" immediately after starting the burn. Once I've completed the burn, I switch back to "Manual axis" -- the periapse of the new orbit and the rendezvous point may shift a degree or two away from each other, but rotating the MFD's intersection point ("R+" or "R-") takes care of that.