It sounds like that for some reason, the monitor adjustments for the screens that are wrong, have changed.
Monitors (modern ones) store the screen adjusments (height, width, etc) that you make to get the pcture to fit the screen size, in a memory inside the monitor. Thus your Windows display at one refresh rate and pixel count, has one set of settings - but your DOS and low res Windows intro screen has another set. This latter set looks like it has changed somehow.
The only suggestions are
To try the default settings button, if the monitor has one, whiilst the screen is in it's "odd" mode - or literally change the height adjutment whilst it's in the odd mode. It should save the new adjustments for this mode, without affecting the adjustments for the Windows mode.
Hope this is a bit clearer than mud!!