When I set a document size, one ruler is bigger than the other. How do I change it to be the same? If I try to make a 4 by 4 square, it shows up as a rectangle. The measurements are accurate but it's just not square. I need to be able to have the measurements on the rulers be the same distance apart,on both rulers.

Can you share an SVG file where that is the case, tell us how exactly you created that file (and if you changed anything related to the 'viewbox'), and also let us know your Inkscape version, please.

This is the first time I've heard this problem, so I probably can't help much.

But I just wanted to mention that the rulers are there only as a guide. Trying to align things to the rulers will not result in precision. Instead, you should use the X and Y coordinates for precision. Or snapping also produces pretty close precision, like snapping to grids or guides. (For me, snapping is often "off" by + or - 0.001, so that's why I say "pretty close".)

Like for example, draw a vertical or horizontal path, and align to some whole number value, using X and Y value of the nodes (Node tool control bar). Then scroll the window so that the path intersects with a ruler. Now, as you zoom in and out, watch how the path is sometimes close the correct value on the ruler, but sometimes not.

For me, it's almost never in the correct place. For me, the rulers are there just for general, visual estimation. But I always use the aforementioned features if I need precision.

While I couldn't trigger the problem either it may be worth mentioning -could even be your monitor setting; does the rest of the screen display fine?- you can set up a document with intentionally different scale factors for x and y (Shift+Ctrl+D).
By using the viewbox tab and changing the default values, I'd expect to change the ruler values too however they stay the same -at least on 0.92.2. Have to admit I haven't updated my version yet; probably that was a bug already corrected.