There's 2 problems. I'm using MechJeb 2.1 and I also have H.O.M.E and Remote Tech 2 installed.

While in manual flight I get this weird oscillation after dropping the first stage. To fix it I have to hit X to drop the throttle 0, then I can use Shift to throttle back up.

The second problem is that after executing a maneuver like a circulation of orbit, the throttle doesn't return to 0 after MechJeb is done. It keeps the throttle up and I shoot past my orbit. I have to hit X to return the throttle to 0 after MechJeb is done.

Here's a video that shows what happens when I try and launch my satellite using the MechJeb functions. This also happens on manned space craft as well.

http://youtu.be/mBF4qZH_gm4
Skip to 2:42 if you want to skip my horrible explanation and just see the problem itself.

If you need anymore information let me know

Have you tried it without RT2 yet? My guess is that it's a problem with
that, whenever the problem itself stems now from RT2 or MJ's handling of
that is another thing.

I have some weird throttle behaviour sometimes too and that only
appeared after I also got RT2.

I always try and get a video. So much easier than trying to explain something. A picture is worth a thousand words right? A video must be worth a lot more then.

I'll try without RT2. Then I'll put it back and try the dev build.

EDIT: ok so I've probably done something wrong. I deleted the RT2 folder and now I can't access any of my saved ships. Clicking on the load button in the VAB does nothing. I assume it's because I had parts that no longer exist.
Ok I fixed it. I just deleted the ship files from the folder and I was able to access the load button again. The game also removed that satellite I sent up in the video.

EDIT: Deleting RT2 has solved the throttle problems. I'll put it back in and try the dev build of MechJeb tomorrow. It's getting late.

The throttle problem with RT2 is solved in the dev build. ( http://jenkins.mumech.com/job/MechJeb2/ ). It's strange that you had it in crewed flight.
The second problem might be related. Can you try with the dev build and tell us how it went ?

And thanks for the video, it's good to have a bug report with info :)

Ok, looks like dev build #129 has fixed the throttle issues. Thanks for the help.