Finally got around to checking the alignment tonight (cos its still pissing down here), I've been meaning to check it for a while but I've had the cruiser up on the platform while I serviced it.

Anyhow, when Id strung up both sides of the rear wheel, though the frame, and measured how much it was out at the front, I couldn't believe my eyes. I double checked my lining up again, same result. It was as if the front and rear wheels were in different planes.

The object of the lesson is, don't pay any attention to the markings on the swing arm for setting up wheel alignment, they can only be considered as a rough guide.

Ill take it out tomorrow to see if it handles any differently.

I have the same issue with my fazer 1000, on one ride the bike felt very  vague on right handers,  two weeks later at the mot we realised the alignment marks are useless,  I now use a straight edge every time I adjust the chain.

and indeed it has made a difference in the handling, also a little less clatter at gear changes.