I would suggest:
1) Practicing playing with an open throat. My first flute teacher always told me to pretend there was an orange in my throat. My current one tells me to open it as if I am yawning. Whatever works for you, you just need to keep your throat open to clear the air passage. You could try setting a timer so that every 5 minutes it goes off and you have to check that your throat is open. This is also a good way to check posture and embouchure or whatever else you might be working on if you want to.
2) Practice tonguing when you play scales. Focus on clarity and keeping your throat open. Articulate with your tongue behind your teeth and make sure your tongue falls to just behind your bottom row of teeth when you have tongued like "tu" (not to the middle of your mouth, this just slows it down).
3) Mix it up, practice different articulations like 2 tongued, 2 slurred; then swap it around, 3 slurred, 1 tongued; swapped; 2 slurred, etc. make some up. it makes it more interesting and is a great way to train yourself with tonguing. You can also practice pieces like this; mix up the articulation patterns to get to know the notes better and practice tonguing at the same time.
JOhnlovemusic's suggestions were also really good. Especially the slurring thing, because you have to make sure that tonguing is just your tongue articulating the passage, not interrupting the airflow - it's not stopping and starting each note. I hope that makes sense... :\
I have had trouble tonguing myself, and still do if I am not careful, and I always go back to exercises like this to help me clear everything up. These are techniques that my teacher has taught me and I find them really helpful. =]
ALSO (last bit i promise!), Jennifer Cluff has a really good website with heaps of good info on flute playing.
have some good stuff on tonguing.
I hope this helps, and I hope you're able to sort out your problem. =]
AND I'm sorry if all of this is irrelevant and not what you were asking about...