During testing for bug #633556 I performed a downgrade to MATE-1.16.x With +gtk3 the notification area of mate-panel has invisible icons which are still clickable. This is a regression compared to MATE-1.18.x which works as-expected.
Setting USE -gtk3 (using only the gtk2 deps) results in a working notification area. I think it's an upstream issue though, since MATE-1.18.x only supports gtk3 and this issue is fixed in that version. I'd prefer dropping bug #633556 and mark these 1.16.x issues wontfix, that way time can be spent focusing on QA / runtesting, etc. for bug #625838 instead.
Created attachment 497818 [details] emerge --info
Created attachment 497820 [details] emerge -pv mate-base/mate-panel This is after setting USE -gtk3 (which resolves the "invisible notification area icons" issue)
GTK+-2 MATE isn't supported anymore. Should you still have problems with invisible icons, please reopen this bug with more information