Yikes. The carve tool is a bit of archaic device for the Source SDK and, as you're probably about to hear from numerous other mappers, is highly discouraged. This is because the carve tool creates a lot of unnecessary brushes and, in the making of these brushes, can create what is called a "micro-leak" - a leak that is difficult to notice. It also makes optimizing a total nightmare.
Even if the point file isn't directing itself right towards an offending carved brush, it is possible the carve brushes is causing the leak. I suggest you remove all carved brush and try to recreate the brushes using vertex editing (Shift + V). You're aiming to get a few balanced brushes rather than a spiral of many little brushes.
Remove and replace those, and if you still have the leak, then report back. Worst case scenario, you can PM your .vmf to me and I'll take a look to see what might be causing the leak.