I have done further digging, and it seems the ultimate kernel cleaner was not mounting the correct devices in order to wipe cache and dalvik cache. I always wondered why the first boot always seems to be just as quick after running the UKC script!
GS2CleanV1.1.zip now gives a true wipe of both cache and dalvik cache partitions along with wiping init.d folder and user.log.
Because of this, do not be alarmed if the first boot takes a long time. (my first boot after this true wipe now takes approx 3 minutes!) This is because a true wipe has taken place, and cache partitions are being rebuilt from new.
I would be interested to hear if this solves the problems old Syd has been having.
I will do further testing, and hopefully get this version up and running on here for you all tomorrow.