This is a known issue, it should be fixed in the next update. In the meanwhile you can use 3.1.4 if you wish. You can always download the previous version from the release notes page.
You may have already identified the cause of the blank space, but I will report it just in case.
It seems that the cause is “MainDocument.nib” in the Japanese resource folder (ja.lproj).
You can drag the collection split to whatever height you want, even if there are no collections in the view to see. It’s like how you can change the width of the binder to be super wide, and end up with blank space to the right of all the names.
Blame Apple for the trend of making split dividers impossible to see and almost as difficult to use.
Great, glad it’s fixed now! This was a crazy bug that I still scratch my head over. I thought I had it fixed in 3.2, but didn’t. It turns out that Apple’s tool for creating UI files in other languages was corrupting the sizing in the Japanese UI file. I had to fix up the sizing in code, which seems to have done the trick. Sorry it took so long for me to figure out what was going on.