I uninstalled indicator-messages because I'd rather have separate icons for my programs. The problem I have now is that pidgin icon won't show up (while others do, like empathy, skype and so on). Or to be more precise, it shows up but is transparent:

When I use the main launcher and there is the dark effect on the top bar, here is how it looks (black square):

To summarize where I'm at with the packages, I've uninstalled:
indicator-messagesindicator-status-provider-mc5indicator-status-provider-pidgin
And systray whitelist is set to ['all'] already.