Pre- Sonar X3, if one has Kontakt installed, it would appear in the browser as something akin to

Kontakt 5 (16 out)
Kontakt 5 (64 out)
Kontakt 5 (8 out).
 
Post-X3 (or, more likely, post X3's VST scanner). these same entries now appear as
Kontakt 5
Kontakt 5
Kontakt 5.

I had to memorize their order :)
 
The same issue holds for Absynth, which also has two entries in the instrument list. Is anyone else seeing this?

I noticed the same. If you go to the plugin manager, you can choose plugin properties and rename them. Look at the file reference box, the output names show up there.

This name change started with X2a. In addition to renaming plug-ins in the Plug-in Manager, changing the value of VSTPlugInNameFormat to 0,1,2 or 3 in Preferences > File > Initialization File can control plug-in name display. 
0 - Format 0:  Vst supplied name which is the new default
1 - Format 1:  DLL Name which is the old behavior
2 - Format 2:  VST Plugin Name (DLL Name)
3 - Format 3:  DLL Name (VST Plugin Name)
Restart SONAR after changing the value. NOTE: To see the Initialization File option make sure the Advanced radio button is selected at the bottom of the Preferences dialog.
 

Nice one Scook!

Ah I had forgotten this option and had dopily wondered why my output labeled names had disappeared after reinstalling X2 and subsequently installing X3. Thanks!