I cannot tell you what caused the problem, but only the symptoms atm. running Xp.

Basic start-up is slow, during the XP loading screen its visibly clear as the loading bar stops starts alot. Genrally slow in most areas but once up and running my computer will run fine, just take a few moments to process everything. Most annoying effect is while playing music the song and words start to slow and stretch while another program is loading (something which its never done before). Ive got PC tool virus scanner and reg cleaner, but isn't resolving the problem. Also for some reason my CD drive is now missing

OK, I wonder if maybe some filesystem issues are occuring, try this and see if indeed there are any and then a fix for this issue.

Click on the Windows Start button then select RUN.

In the OPEN line type in cmd as in command and then click the OK button.

A command shell window will appear, type in the following command without any switches, chkdsk and press the ENTER key.

It will run chkdsk in READ only mode but it will tell you if any errors were found and to run the command again with the /F switch, please do this if neccessary and press the Y key to schedule on a reboot, then reboot the machine and see if this fixes the issue or not.

You can also use the /R switch to test the unallocated space too but it will take longer to scan as it will check the entire partition.

you may have some heavy programs installed in your system which takes a lot of memory. check the task manger and see which process is taking a lot of memory. if you have installed any heavy software recently then uninstall it.

If you notice that your machine seems to run fine after you've been logged in for a while, it's usually due to the startup scan initiated by your virus when you boot your machine and the OS loads. In addition, you may have a bunch of apps/services trying to load at the same time, which consumes a lot of your CPU, causing the entire system to crawl.

james brown may be correct with the apps you have running, which could cause the sluggish behavior with your machine. Often, applications that are installed make themselves load on startup and run in the background, which hogs up system resourcecs. Click Start | Run, then type in msconfig. Go to the Startup tab and look through the list; my guess is that you have a lot of things in there. If you recognize apps that are running but not needed (e.g. Adobe speed loader, Quicktime/RealPlayer scheduler/updater, Logitech utilities), uncheck them. If you don't know what something is, do not uncheck it without looking up what it is and if it's needed. After you click OK, you'll have to reboot your system.

Be very careful when making changes to msconfig, as you can mess your system up if you aren't careful, although you can reverse the changes. Best to not touch any other tab except Startup.

Also be careful when running CHKDSK. It tends to delete "orphaned" files, which I've had cause issues with the system (a.k.a. deleting files that were needed). From my experience, it's best to use CHKDSK as a last resort and make sure you have a good backup of your system before running it. The read only mode that jmmijo mentioned is a safer way of running it.