Right then Johnny....heres my thoughts on this for what its worth..(the Daves will be along soon I hope!!)
You know something isnt quite right and a wire is crossed somewhere or the likes..this is what my simple brain is telling me to do.
1. IGN OFF, BATTERY DISCONNECTED.....remove each fuse in turn, reconnecting battery and switching ignition on each time. If you find that removing a fuse cures it, or stops it happening then you may find the offending circuit thats interfering. Remove the fuse for the circuit in question and see if it stays on. You will know then that the feed is from another circuit somewhere.
2. Draw a very simple schematic from your shop wiring diagram of just the circuit you are looking at fixing. Mark the colours or draw it in the colours as per the book.
3. Using the diagram, check each wire in that circuit to make sure it goes where it should, is attached to what it should be attached to and isnt shorting out any where. Thoroughly clean everything as you go along
That might be a starting point for you
Is the flasher relay for your indicators or your hazards? Have you tried a new flasher unit (sometimes a spare under dash) or have you tried swapping them over? Try one plugged in and one disconnected, then swap. Try testing the feed out of the relays....should basically show 0V 12V 0V 12V 0V 12v etc.
Just thinking out loud as we need to get you sorted.