That suggests that you didn’t do some part of the wall straightening perfectly. It all worked fine when I did the same.
I’m now having a problem when I try to straighten the wall.
Sorry about this btw. As you can tell, I’m still learning the program.
Lock the direction of movement using the appropriate arrow key before you attempt to inference to the bottom corner. right = red, left = green, up = blue
Here’s my process. Can’t find where I’m going wrong.
Here you can see it isn’t consistent on each rectangle either.
Here is the process, sorry.
Edit: It seems my gif might be too long to upload.
https://drive.google.com/file/d/1OcejBtYDEa5_wth25ZKRFaoiq9bOQlBl/view?usp=sharing
Here’s a link for you.
To me it looks that some of your guides are on the face and some are not, and that the other side of the wall is not quite parallel with the front side. Instead of struggling, I would probably have redone the thing.
I think you might be right. Thanks!
One thing: Turn off Length Snapping (Window menu > Model Info > Units).
As @slbaumgartner points out the distance from origin makes the difference here.
Here’s your model as uploaded.
Redoing the wall is the way to go. Thanks everyone! If this doesn’t work on another wall I’ll post back here.
Never thought of this. Thank you!
Not sure how you drew your model in the 1st place but normally the best way is to draw a 2D floor plan then use push/pull tool to extrude it all at once to the desired wall height. This ensures that (a) your floor plan was sound from a drawing standpoint (otherwise push/pull wouldn’t work) and (b) your corners are straight and your walls are plumb.
It is often (OK, almost always) easier / faster to erase and redo janky geometry than trying to fix it.
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Off-topic - which screen capture app are you using? Good quality - good file size. Thx!
Of course it is important to learn why your model was not ‘behaving’ when you tried to cut the window openings: Now you know that the inner wall surface was not in plane with your outer wall surface… but, be sure not to lose the other lesson here… what if that was your original intent, say, to design a wall that was 12" thick at the bottom, and only 4" thick at the top, and you wanted to cut a window through that. The method required would have worked for your problem as well so if you were not concerned about the parallel orientation (such as when doing a ‘quick and dirty’ drawing, rather than spending the time diagnosing and fixing the problem, you could have done this: Draw your rectangle on one of the surfaces, and push well past the other so that you had a ‘box’ sticking out the other side of the wall, then orbit until you can see the other surface, select it, and then choose Edit/intersect faces/with model and then just erase the extended box and the created surface inside the window, and voila! You have just cut a window opening through a tapered wall. 
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It is good to learn the right way first as above, then you can save yourself a lot of time by using a plugin. SEE Adding a Window using PlusSpec
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This is how I first drew my model. You’re definitely right in that redoing the wall is the best way to go. 
Works great!
Funny you say this actually. The day after I first posted this, I asked my teacher what was up and he walked me through this exact solution lol.
I appreciate it!
If I hadn’t mentioned it already, this was for a high school course and I was only doing it the way my teacher had taught us.
If I ever decide to model another home, I’ll definitely use this guide.