I specify 1 colonist resource and 2 rep for kloning a kerbal but I'm finding that 2 rep and 2 colonist resource are being used up. This 2 colonists happens in sandbox mode too.

Ill do some more investigation with vanilla resources tomorrow

Still waiting on time to look into this vanilla

Definitely does this with vanilla - The VAB shows the correct (specified in the CFG) amounts of say 50 Ore, 50 LF, 5000 EC, but when kloning on launchpad uses double these amounts.

two things: what difficulty and what is the game setting for global multiplier?

Not sure about game setting. Default i guess. A Normal save game career, no changes to multipliers. Ill have to check game settings