Adobe Media Encoder, rendering wrong videoparts from waitinglist

Hi guys,
I have a small, but pretty anoying problem.
So I'm a normal hobby like Youtuber,
rendering a few video series I created over night.
So I cut und edit them in Adobe Premiere and then I press ctrl + m select 720p and put them on the waitinglist in AME.
Because I can render them all over night like this, or I can render, while still editing other videos.
I usually but all my video parts in one sequence in Premiere, and then cut then like in 15-20minute parts, using the In and Out markers(and then select Sequence In/Out in Rendersettings)
But the problem I have using this method is,
lets say I have 10 videos on the waitinglist of AME, it renders like 3x Part 2, and then part 4,5,6 and maybe 2x part 8 and so on.
So instead of rendering them all like I marked them to, I get a few of the parts duplicated.
And its not a problem of me marking them wrong, because its in every rendering que I do.
And its alsways random which parts get duplicated, but i can be sure there will be a wrong part in every rendering que.
So the only thing I can do right now is either rendering them all one by one directly in Premiere.
Or selecting the false ones again and putting them back onto the waitinglist.
But its so anoying.
Especially the first time I havent´t checked them, so I uploaded them right away, and saw oops sth. went wrong.
Does anyone have any solution to this?
I´m using CS6
Thanks for your help.

When I say render, I'm referring to rendering inside of Adobe Media Encoder - unless there is something I don't know when it comes to the setting you're referring to.
Also, yes, it has an animated logo - which I use on the other machine too, same exact animation.
As I was writing this response, I just disabled the logo animation - it renders in 4 minutes. However, I need this animation - I'm wondering what to do. It has a 4Kx2K png animated using the basic 3D effect and HLS effect - though, this doesn't delay rendering on my other computer!??
Hmm, thought of a fix though, I’ll render out my logo animation with a transparent channel, this way I just drag the scaled down animation on top of my videos, should improve the render time.

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