I just got my MacBook Pro less than a month ago, and I'm experiencing the same issue. I haven't done anything with my fonts. It seems like it could be a memory issue as it starts happening near the end of the day after working on my laptop all day. I am a web developer and usually have TextWrangler, Firefox, Thunderbird, iChat and iTunes open most of the day. And sometimes I'll use Photoshop. I have 2Gb of memory, and whatever the standard video memory is..
I've never experienced it right after booting. It affects all programs and have even seen it on the top system menu. I've noticed it when writing code where the "gap" will stay at the same spot on the screen. So if I'm inserting text at the beginning of a line of code, the "gap" will stay at a spot, say 20 characters in. So as I type, and the characters are being pushed right, the "gap" stays in the same spot. So it's not that certain letters are disappearing, but rather that certain spots on the screen will just stop displaying whatever character should be there. But it's also on a per-window basis--if I drag a window around, the "gap" will float with the window.
Hope that makes sense...