After reading a little about digital audio, I'm putting this issue down to a faulty HDD. The fault did not appear to be a sound system fault but was more of an interference fault which was triggered every time the HDD was activated or when software on the HDD was activated. The HDD did have some serious issues which were causing very slow seek and read times although I don't have any way to measure the speed before and after, it was getting slower all the time and was excruciatingly slow towards the end. One test I did manage to run reported it had "A few bad sectors" but it was at least 10 years old !
Switching to a new Seagate Barracuda has vastly improved
performance and there are no such issues, I'm just happy that I managed to switch over and transfer my important files before it completely died.
I can now mark this as SOLVED
So that's another fault solved and in the process of sorting out a number of faults in the past few months, I have replaced every component in my PC ! PSU (twice), Motherboard, CPU (twice), RAM, GPU, HDD and fans, I also decided to upgrade my monitor so I might as well upgrade the case too
Processor: AMD FX -4100 @ 3.60GHz (4 Cores), Motherboard: ASUS M5A78L-M LX V2, Chipset: AMD RS780 + SB7x0/SB8x0/SB9x0, Memory: 4096MB, Disk: 250GB Seagate ST250DM000-1BD14, Graphics: NVidia GeForce GT610 2048MB (810/500MHz), Audio: Realtek ALC887-VD (Audio still not properly configured but working perfectly).
Case; Silverstone Temjin TJ08B-E
OS: LinuxMint 12, Kernel: 3.0.0-30-generic-pae (i686), Desktop: KDE 4.7.4, Display Server: X Server 1.10.4, Display Driver: NVIDIA 280.13, OpenGL: 4.1.0 NVIDIA 280.13, Compiler: GCC 4.6.1, File-System: ext4, Screen Resolution: 1920x1080