Login Start-Up Problems
As @Hippo noted, you're probably talking about the OS X Lion feature where programs that are open at shutdown are automatically re-opened at startup unless you uncheck a checkbox when shutting down. Currently, there's no way to unselect that choice via the default UI. 

However, a few posters in an Apple Discussion forum have provided some Terminal commands and created AppleScript scripts that can perform this task. 

Terminal Solution

Scott Nash wrote:


  
  Open up your ~/Library/Preferencese/ByHost folder and delete
  the com.apple.loginwindow.&lt;long alpha-numeric string&gt; 
  Copy and
  paste this command into Terminal:
  
  defaults write com.apple.loginwindow TALLogoutSavesState 0
  
  
  The file you deleted is the one that stores
  which apps and windows are open. The command directly writes the
  preference for saving the logout state.   
  
  You can read the setting by
  using this command, although it should reflect the setting in the
  General System Prefs, now. 
  defaults read com.apple.loginwindow 
  Look
  for the line with TALLogoutSavesState. It should be 0, now.   
  
  The
  checkbox in the shutdown dialog will remain checked, but you won't
  need to change it. It should ignore that since the main preference is
  set to not save state.


Script Solution

Vic07 wrote:


  By using a simple AppleScript application, you can achieve this in a
  consistent way.   
  
  I've compiled an application that after clicking its
  icon, it will shut down your Mac with "save state" disabled. You can
  use this app on a daily basis instead of turning the Mac off in the
  traditional way.   A good idea could be putting it on your Dock so you
  always have it handy.   
  
  You can download the app from here


Later in the discussion, he posts updated versions:


  CleanReboot and CleanShutDown have been updated to 2.0.   
  
  This new
  version is /MUCH/ cleaner than the previous one, since instead of
  modifying the defaults it makes Finder act like if the user unchecked
  the save state checkbox and then clicked the Shut Down or Restart
  button.   
  
  CleanShutDown 2.0
  CleanReboot 2.0


You may want to check out those scripts to see if they address your issue.

One of these two methods may address your issue - I'll have to test it on my Mac after I head home.