With the Acrobat/Reader 11.0.10 and 10.1.13 update (on Windows), every time a user logs on to a computer, a new RunOnce registry key is created. While this new key is not actually launching an executable and would not slow down system startup, it does cause third-party programs that monitor such key changes to display an alert.
This problem does not appear on Mac OS.
Run the msi installer posted here. Restart your computer, if required.