Check your flute has no leaks. I had that problem with my older Gemmie, until I had it fixed.

I have the same problem. One day, i'll have good tone but then the next day it's terrible. It's the same with tune. I've also tried messing around with my embouchure and breath support, but it doesn't seem to be making a difference. I've also tried opening my throught a little more but I usually just end up loosing control of my embouchure doing that. I hope someone can help me with this too.

I know this might sound pretty bad, but take a break from it. I had this happen to me about a year ago. I couldn't play if my life depended on it because my tone was so poor! I couldn't get it back to where it was and no matter what I did, it wasn't helping.

So, I'm not saying give up on it. Put it down for a bit. If you have band or any other musical classes/groups where you have to perform in, still play, but don't go over the limit. Knock a few hours off your practice plan a week for a few weeks and then start to increase again when you feel like you have more of a control over your emboshure. This worked for me, but might not work for everyone.

Perhaps try playing another instrument, too. When I picked up the drums and the trumpet during the time I cut back on the flute, I found myself much more musically inclined. "Reviving the spirit" helps like you wouldn't believe!

Pad leak in my Gemeinhardt M3 were also temperamental at the beginning, then the pad degraded too much and the problem became permanent (I had it replaced).

Taking a rest does help, at least sometimes. After a long practice (in my case, just one or one and a half hour), I am tired and the tone quality degrades noticeably. If I leave it for a couple of hours, it comes back. I believe its is related with face/mouth muscles not being able to work as they should when they are tired. I know more advanced students and pros can play much longer without becoming so tired, but their technique is obviously better (and they are probably younger).

Leaving the practice for a couple of days can also work. I do not know the reason, but it could be worth trying it.

Also beware that if you feel too much anxious to stop just for a couple of days, you might be stressing it too much and this could not be helpful.