I just recently pulled my game The Movies out again and it installed just fine and the auto run menu even comes up when I put in the DVD-ROM, but when i click to play, it says please insert the DVD/CD to play.  Whats the deal?  I cant get past the autorun screen.    

I had this happen with an ASUS DVD drive. It installs / plays DVD movies just fine, but when a game has to detect the disc in the drive... it never does. The only way I've got around this is by downloading a patched executable to bypasses the DVD reading part.
 
I'm going to take a guess and say that your drive is also a SATA drive?

Yeah it is a SATA.  I have never had this problem until installing my old Movies game and also my COD4.  Good thing I have two drives though, because COD4 worked in the older drive.  Still the Movies game doesn't work in either.  

I have this problem with Bioshock.  I have to stick the disc in and start it from the menu that pops up from autoplay, then press Play on that menu.  If I have the disc in the drive and try the icon on my desktop...no go.

 
For you, I may have an idea.  Find where your main Bioshock folder is and open the folder.  Find the main executable file and try making a new shortcut.  Just right click on the executable folder and click on create shortcut.  I dont know if you have tried that or not, but it may be worth a shot.  Maybe your older shortcut become corrupted or something.  
 
I wonder if there is something we have to change in our executable file.  For example adding something in the proporties of the shortcut.  I haven't found any solutions yet.