Hi Robb F,
In short, you need to keep a log book, take picture, and write down everything you say, everything that's said to you, whether it was 'done' in person or via phone, and start a paper trail!!! IF you end up in court w/your builder, the judge won't decide on he-said, she-said. He's gonna want to see SOME effort at documentation. There's no need to 'alert' the BUilder in ANY respect. Just make notes after his visit or phone or inperson phone conversation.
Now, in the meantime, if you have a Warranty on the home, EXERCISE it. Re-read it to see what you're allowed to do and what he must do. Also, consider asking your neighbors (if you're in a sub-developement) if their homes by the same builder have the same problem.
RE: The Great Room Window, it sounds like there is a problem w/the Flashing. It is what keeps water from getting in/under the window frame.
RE: The basement windows, since the window isn't finished, it may be just for that reason that it's leaking. BUT, depending on what you mean by 'not finished', there may be a problem w/the flashing too (but then it could be something else.) Who knows. Tracing water leaks is an art and the 'fix' is sometimes best served by just redoing the whole project. Just start documentating and read your Warranty. I wish I had better news.
My best to ya and hope this helps.
Jay J -Moderator