I can’t explain all of the problems, but a microphone system change can do magic things by accident.
Zoom repeatedly until you can see the individual up and down motion of the stereo blue waves. (Control-Scroll??)
http://manual.audacityteam.org/man/zooming.html
On a normal sound segment, I expect most of the up and down blue waves to be going the same direction. I expect yours to be opposite.
Describe your whole microphone system. Connecting a higher quality XLR microphone to a computer system wrong can do this.
Koz