It happened on my old PC and it still happens with the new one, with a fresh Ubuntu 12.10 installation (Unity). When returning from a screen lock (I couldn't say if it can be replicated in other ways), some indicators are missing: pidgin, thunderbird (with firetray extension), jdownloader...
I don't know whether those indicators have something wrong regarding unity's tray or something related with global menu is cutting out a certain size of left edge of a long tray, whatever it contains.