As don_crissti suggesteddon_crissti suggested, I was missing the WMCLASS key within my .desktop entry. Without this, the DM(here beign Gnome3.6) failed to match the windows together with the specified menu entry. The launcher now groups all subsequent instances of Eclipse together now.
From what I've read about the .desktop file specification, here, is that the optionally extra key specified during the launching process provides an identifier to match other associated top-level(parent?) windows with:
WMCLASS
a string to match against the "resource name" or "resource
class" hints. If this key is present, the launchee will most
likely not send a "remove" message on its own. If the
desktop environment detects a toplevel window mapped with
this name or class, it should send a "remove" message for
the startup sequence.
And further on within the document:
StartupWMClass=STRING
If true, it is KNOWN that the application will map at least one window with the given string as its WM class or WM name hint.
