At first, i thoguht it was my microphone so i tested it with another microphone but the same issue occurred.
I then thought it was my sound card as I have a new computer and my sound card had originally played up, so I purchased a cheap new sound card and chucked it in my PC only to find out it made no different and in the process, i made my PC warranty void because I opened up the case.
I then realised I recently upgraded to the latest version of Skype (v2.4) and then started to wonder if it was Skype itself that was causing the problems.
I then turned off the auto adjustment option but this didn't achieve anything.
I then decided to downgrade to the previous version of Skype and this solved all my problems.
Since then, I've found out that many others have had the same issues and many others have had to downgrade to the previous version of Skype.
If anyone is suffering from the same issues as I did, i hope this helps you.
For the majority of users, this probably won't effect you. My understanding is that it only impacts Windows 7 users and only when there is an application or game running in the background.
The latest version of Skype is also annoying because it keeps the software active in the task bar (you can't minimise it to the tray) - this is for Windows 7 only as far as i'm aware.