Or a note that updating status via pidgin updates your "online" status, not your status?
Sorry to be dumb about this, it's my first wiki edit.
Ever since we updated sipe to 1.15.0 (or the interim version 1.14.x) Pidgin clients have been occasionally showing users offline even when they are online.
We have a mix of Windows Lync, Mac Lync and Linux pidgin/sipe clients (totaling at about 1300) connecting to the Lync server.
So, long story short, if opening Pidgin from the messaging menu gives you that trouble, use the solution listed here.