I have now managed to fix this, well at least get it working again. After checking through the trace logs I found that I was getting a Dynamic compression error. By removing this from the sites users are now able to browse again.
-> Take IIS backup.
-> Open IIS
-> Click on server module node at the top of the left hand tree and choose “Modules”.
-> Right click on DynamicCompressionModule and choose “Unlock”
-> Right click on StaticCompressionModule and choose “Unlock”.
-> Open desired websites -> Open Modules.
-> Right click on DynamicCompressionModules and choose “remove”.
-> Right click on StaticCompressionModule and choose “Remove”.
-> Do an IISRESET.