I've noticed it shortly after I updated, but it was when gtk+ 2.18 hit gnome overlay, so it was long ago and it just motivated me to switch to ibus. But, since this will get noticed, I'm filing it anyway. This is obviously an upstream problem, caused by client side windows. I took a look at scim sources and it seems fixing that won't be trivial (instead of using that env var override). Problem is simple: tray icon no longer shows up in the tray. scim works anyway.
If you are still suffering this bug, please try patch from: http://launchpadlibrarian.net/36866242/scim-fix-disappeared-status-icon.patch
It's the same, and is solved applying the patch *** This bug has been marked as a duplicate of bug 283317 ***
