From your description, and without a screenshot, I'm guessing that you have an object with text wrap turned on that's forcing the text to move, because that's the behavior you would see in that case. The object may be transparent or invisible (no fill or stroke), and on any layer.
If that is what's happening, open the text frame options dialog (Ctl/Cmd-B) and check "Ignore Text Wrap" and the problem will go away. While you're there, verify that the vertical justification is set to "Top."
Another less likely possibility is that you've accidentally changed the default paragraph to full justify.
An even less likely possibility is that you have accidentally set a default Object Style that plays havoc with your text.
Finally, if it's none of the above, use the BITS (Basic InDesign Trouble Shooter) technique: Save As an IDML file, then open that as a fresh InDesign document. This removes any cruft that may have accumulated in the document in the course of editing and gives you a clean new copy to work with.