I recently installed the Opera web browser, and had strange focus issues that reminded me of the problems I had with urxvt and scim in the past. After trying their latest development version and lots of searches, and not finding any bugs, I concluded it was probably my set up again. I disabled scim and sure enough the problems disappeared.
After some research, I discovered a couple of other input methods: uim and ibus. I tried them both out and had better luck with ibus - I was able to get traditional chinese using pinyin input working better (using the Chewing module). It seems like uim and the ibus-pinyin module are using a Google pinyin input method which is probably better for natives but just confuses me.
Getting it working was pretty easy, just install the ibus-chewing package, run im-config and select ibus input method. Restart your window manager and then run ibus-setup to set the hotkeys and the input method you want to use. The only tricky part is that I had to enable chinese input and then click on the preferences icon the change the input keyboard to Hanyu.
For now, it appears my focus issues are solved.