Secondly I did the diagnostics test with the alligator lead and all the switch numbers were coming up fine until I got to pin6 on the 2J2 header.
Before then just 1 number would appear and then sequentially decrease as I moved down the header as it should indicating that particular switch number, but shorting out pin6 on the 2J2 header with any pin on the 2J3 header would give all sorts of odd numbers , but then move the alligator lead down to pin 7 on the 2J2 header and then the sequential decreasing of switch numbers would continue again all the way down to 1.

So , it would appear to be a fault with the board.
A visual inspection came up all ok, no broken tracks or shorts on the board.

Mate, pin 6 is the key pin on 2J2 on the Rottendog board as far as I can tell.
I assume it shouldn't be tested as it would give strange readings.