I've had the same experience so I know how it feels.
You said the feeling is happening on the freeway with grooves in the pavement parallel to your direction of travel and it happens at higher speeds. The first thing I would do is find a road that does not have these grooves that has a higher posted speed limit and see what happens. I'm thinking the feeling will go away. Any time the road surface changes, so does your contact patch on the tires. A bike naturally weaves a very subtle "S" track as it goes down the road, even when you think you are going perfectly straight. As it does this, it crosses over the grooves and the tire contact patch changes slightly, causing the bike to alter its natural "S". I think this is what you are feeling.
There is one section of similar road near me and I know the first couple times I was it, I had the same feeling you do. It was VERY unnerving. I went slower and was almost scared to turn/lean.
I then switched tires for the stock dunlop to a PR3 and the next time I was on the road, the feeling has pretty much gone away.
Some of that may be attributed to the tires, some to just having more experience.
Last summer I rode across the Mackinack Bridge. There was construction in the outer lane so I had to ride on the 2" grate surface of the inner lane. Yes, you can look straight down and see water way down there, don't drop anything, haha. Anyway, I've heard people say that it is very unnerving to ride on. I didn't have any problems, just stay relaxed and let the bike do its thing. It wonders a little but that's ok.
Try a different road, try changing your suspension (I have no experience here so just going on posts above), try different tires, and get more experience.
P.S. I see ZX6R posted while I was typing. Sounds like we are thinking along the same lines.
Last edited by Slow-Steady; 01-04-2014 at 08:59 AM.