Vista - Have to boot up using disc

Ever since I got rid of 2 trojans that Threatfire found (they came in with an Incredimail installer and a Photoframe Installer) I have to use the installation disc to boot up. If I run checkdisc it says that "no problems have been found". If I take the disc out and boot up, everything seems ok for about an hour and then everything freezes and I can only get out by turning off the power by holding down the button on the tower for 4 seconds. I have tried to click on F11 to do a Repair but it just boots up as normal. Will it do my OS any harm to keep booting up from the installation DVD ? I am also using McAfee total security, Windows Defender and Superantispyware (no "nasties" found) and I have uninstalled Threatfire as it seemed to be causing conflicts.