After installing mechjeb 2.0.9, while sitting on the launch pad my horizontal indicator is not indicating that my ship is vertical, its leaning to the west by about 10 degrees (although my ship is on the launchpad and is obviously vertical). Also, the indicator for my AP is freaking out and flickering all over the horizontal indicator. Any one have any ideas? Any help would he very much appreciated.

Is the mechjeb box on a slanted surface (side of pod, ect.)? It's possible that your craft is accidentally being set to be controlled from mechjeb itself, and not the pod. Try right clicking on the pod and setting "controll from here". If that fixes it, then that was the problem.

That was it! The Mechjeb was on a slanted surface and i didnt realize it. Thank you for your help!!

You may want to ensure that you're controlling from the correct part if you're concerned with accuracy or RCS efficiency, as KSP will probably try to rotate the whole craft around the mechjeb box if it's leading.

I made sure to right click on the pod and to select "control from here" problem seems to be fixed. Only lasting problem is the sever bobbling and eventual explosion of my ship if i leave the Mechjeb on for the entirety of the launch. Most of the launch i manually control the ship, then i use the mechjeb to get my orbit circularized. Thanks a ton for the help guys!!

Use struts between weak links, and find the "smooth throttle" check box. That will help with the "pogoing".

Ship* sorry.

Ive got six struts that i put on the weak parts pf the shit, still no effect. I also checked the smooth throttle box as well. Cant seem to figure out how to get mechjeb to stop all the intense minor corrections it seems to do which is what i think is causing the "pogoing"

Closing this as an old MechJeb issue. Many MechJeb issues have had little interest in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is. This issue is being closed for one of those reasons. We apologize for any inconvenience, but keeping the TODO list tidy helps the developers.

If this bug/issue is still a problem, please open a new issue. For bugs please try to include a Minimal, Complete, Verifiable Example that explains all the steps required to replicate the issue. A link to the KSP.log file should be ideally included, but is often not sufficient information. Screenshots or short videos are often the best way to show a bug.