I assume the huge reject rates happen when the pool switches to some crap coin with a block rate that is too fast for its own good. Upgrading to cgminer 3.7.2 from 3.4.2 and using intensity 16 instead of 18 seem to have helped bring my reject rate down overall, but I still see 10 minute intervals of 30-60% rejects which results in 10-15% rejects for the hour.

I guess it is still better than mining LTC if I get 15% rejects and the pool is doing 120% of LTC or better for that hour.