I had this trouble with U-he plugins, but it was fixed several months ago, by U-he, as I remember.
I just tried this, using Manchester and Zebra2 version 2.7.2:
Open Save Preset dialog in Zebra2.
Type d. Sonar treated it as a shortcut.
Change Give all Keystrokes to Plug-in to Enabled.
Type d. The letter d appeared in the Save Preset dialog. Sonar didn't react.
Are you getting different results from this procedure? Are you using U-he plugins?
Mitch I.