NV, I just saw your post; I JUST had this same conversation with my teacher last week!!!  Mine took a little longer to occur, but same issue.  For 3 months, I had been diligently practicing, and felt pretty sure of [pretty closely] where my fingers should be.  Then, all of a sudden, I began feeling somewhat "dislocated" on the fingerboard.  I began wondering if what I was hearing was right or not.

Here's my teacher's explanation; he believes that people experience this problem because they actually start hearing more accurately.  He thinks that at first, as long as you're intonation is close, your ear really can't distinguish more minute adjustments.

Have you ever been on a long journey to a new city… at first, you're just happy that you found the right city,,, but then you discover that you really aren't exactly where you want to be in that city, so you experience some degree of anxiety until you've found the exact street that you want to be on, and then you experience a certain degree of satisfaction and content that you've found the right street,,, but then, more anxiety because you haven't yet found the exact apartment or store that you want to find,,, until eventually you are EXACTLY where you want to be.

I have always used a pitch analyzer to tune my violin, and occasionally to check my intonation while practicing; but I now spend the first part of every practice session using my pitch meter while slowly running through my lesson, making sure that my intonation is accurate.  I place it on my music stand right under my lesson and monitor every single note.

That's how I'm dealing with this issue…. it's helping a LOT!  Don't get discouraged, you WILL work through this.  Yes, it is great to have a pro [teacher] who can detect intonation immediately.  My teacher is my immediate, human, pitch monitor.  But, for lack of a teacher, get a good pitch analyzer; if you don't already have one, FM has a couple really affordable units.