Hi,
A full installation should only access the CD for cinematics and as part of the safedisc protection on startup. Accessing the CDROM drive during the game would certainly result in lag, especially if the drive is idle.
Here are some suggestions,
Check the installation size (minus size of the run\dynamic and run\savegames directories), reinstall, and see if that fixes the problem (did reinstalling change the installation size?).
If that fails, search this forum for information on installing the game by manually extrating the .rar archives contained on the installation CDs, using a program such as WinRAR. Try the FAQ under technical support.
Alternatively, if you have the room, you could use a program such as DAEMON tools (search the web for it) to create a virtual CDROM drive from an image of the play CD.
Good luck!
-Fabian