Wow, that will teach me to not check on the D&D Rules board for a few days! (And by the way, I saw someone with the .sig "Every time I go to the D&D Rules board, I think, 'Yes, it sure does,'" and although I can't remember his or her name right now, for which all apologies!, I have to say that that is an excellent line.)
I'm the original designer of the Arcane Thesis feat. I say original designer because the version that appears in the PHB II is different from the feat I designed. This is a normal consequence of Wizards' development process, and every book, without exception, benefits from their development. I point this out only to act as a caveat to what I'm about to say. Which is this: I shouldn't be taken as the final arbiter on this feat; I was only a small piece in the process of bringing the PHB II to you.
For what it's worth, then, I would rule as Majoru Oakheart does (see his posting just previous to mine). Each metmagic feat applied to a thesis spell adds 1 level less than normal, with a minimum of 0 levels added. Thus, if you apply one metamagic feat with an adjustment of +2 levels to your thesis fireball spell, then you end up with a 4th level spell. If you apply two metamagic feats with adjustments of +2 and +3 levels to your thesis fireball spell, then you end up with a 6th level spell. If you apply four metamagic feats with adjustments of +0, +0, +1, and +3 to your thesis fireball spell, then you end up with a fifth level spell.
Personally I think everyone who takes the feat should also record the name of his thesis:
Fireball and the Kobolds of the Caves of Chaos: Forty-Four Case Studies; Melf and His Arrow; How Magic Is Your Jar?. Bonus points if you write out the first paragraph on edge-burnt parchment and insist on thrusting it into the hands of players at the table saying, "Read my thesis, read my thesis."
