Since the problem is [still current] as of Adobe Acrobat XI version 11.0.10 and in athe 'Pro' edition
The regkey to change to prevent Navpanes from showing up (on the Left of the Document window) when opening a PDF document is:
HKEY_CLASSES_ROOT\Acrobat.Document.11\shell\Open\command
Name: (Default)
Type: REG_SZ
Data: "C:\Program Files (x86)\Adobe\Acrobat 11.0\Acrobat\Acrobat.exe" /A "navpanes=0" "%1"