This will show you shares that might have otherwise been valid if you were not mining merged. cgminer does not submit them so your stale rate actually will not go up as DeathAndTaxes suggested unless you enable the --submit-stale option. (I don't suggest you do).
Any reason why?
Also background on why I recommend enabling "--submit-stale" for those who may not know is for the following scenario:
1) your find a BTC share
2) the pool detects a change in NMC block and issues an LP
3) if you discard the work you discard a valid BTC share
4) if you submit it you gain a valid share.
now if the LP is because BTC block is invalid then yes you are submitting a stale share but you don't lose anything. Instead of a SS locally you get a R but it doesn't negatively affect how many valid shares.