Strange Maneuver Node Issue

[VelvetGentleman]

I'm not new to KSP but my previous attempts had all stopped pretty soon after the basics. This recent foray has hooked me deep however and I can't stop playing. After exploring Kerbals SOI for and sending probes to other planets I figured it was time for an extrakerban lander mission. But seeing as how it wa a special occasion I wanted to build something equally special so I decided on an Apollo style mission to Duna with the landing vehicle attached under the third stage, even though I know it isn't the most efficient. After much grief getting it into orbit and docking the lander properly I was proud of myself and everything looked like it was going well. I plotted my first maneuver out of LKO which would give me an encounter with Duna. This is where the weirdness began. The burn time was reading a little over two minutes which I thought was a low but this was the first time I'd used the nuclear engines so I ignored that. Then I remembered I had set my third stage thrust to 10% to perform the docking, but when I put it back to 100 my burn time jumped up to three minutes. I thought it was just a bug with not setting my thrust to 100 before making the node so I redid everything and it still three minutes and it would go down to two if I reduced thrust. Weird. So I decided to ignore it and just burn... and the burn counter decreased by about one second every ten actual seconds. So I restarted the game, redid everything and had the same issues. I figured my setup had broken the game's calculations or something so I installed MechJeb2 to see if its burn timer would be more accurate. So when I had it installed and everything was was plotted out again my KSP burn timer was reading 2 minutes and change but the MechJeb burn timer was reading about 16 minutes. I did the MechJeb burn and it was way off, I'm assuming because it was using the KSP target indicator which was positioned for a 2 minute burn the whole time. I set the engine on the lander to independant, and I disabled it completely, both of which made the KSP burn time fluctuate still in the 2-6 minute area. At this point my excitement for having an Apollo style lander has completely hit a wall and I'm tearing my hair out. I really want to get this thing to Duna but I don't even know where to start at this point.

 

The mods I have are fairly basic. I have visual enhancements, Precise Node, Kerbal Alarm, Kerbal Engineer, Stage Recovery, and now MechJeb (though I plan on removing it once this is sorted). 

[vossiewulf]

Did you try removing Precise Node? Because if I'm having a weird maneuver node problem the first thing I'm going to suspect is you know, the node mod I have.

Otherwise have never seen something like that. And you should really keep MJ installed, if you haven't already you should look at all of the things it can do for you. It's very good at interplanetary transfers, for example.