I upgraded from 17.10 to 18.04 today, and I still have this problem as well.
In response to comment 21:
Is the icon really giant (144x144) or smaller (48x48)?
It is smaller after the upgrade to 18.04.
Does installing/removing gnome-icon-them do anything for you?
Yes, installing the gnome-icon-them as per comment 8 appears to fix the issue; uninstalling the gnome-icon-them causes the issue to return.
What size is the icon reported as when executing xprop from gnome-terminal and clicking on the gnome-terminal window?
When the issue is present, xprop reports: _NET_WM_ICON(CARDINAL) = Icon (48 x 48):
I upgraded from 17.10 to 18.04 today, and I still have this problem as well.
In response to comment 21:
Is the icon really giant (144x144) or smaller (48x48)?
It is smaller after the upgrade to 18.04.
Does installing/removing gnome-icon-them do anything for you?
Yes, installing the gnome-icon-them as per comment 8 appears to fix the issue; uninstalling the gnome-icon-them causes the issue to return.
What size is the icon reported as when executing xprop from gnome-terminal and clicking on the gnome-terminal window? ICON(CARDINAL) = Icon (48 x 48):
When the issue is present, xprop reports: _NET_WM_