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).