I'm having file upload problems also. I think mine are a bit different than yours, But I suspect /mod/file/actions/upload.php is the culprit to.
I looked at my /data/2011/ and its chmod to 700. uploads work fine for me, except for mp3's.
Still searching. So I think I should edit engine/lib/filestore.php file. There is a lot functions. But still can't find where to add chmod().. And my mistake in first post. Directory is created with 644 permissions, but still it's not good bacause files is not stored in subdirectory. Directories permissions should be 755
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