Are you losing your low flushes with SCs (say 5,6s)?
I used to have this problem in spades (and in hearts, etc.)
I haven't had this problem once since I changed to playing SCs like big pairs. I raise with them (granted I play 6-max) or I call a raise with them. Hence, I'm usually against a big pair and when I make my flush, I'm gold.
If I limped, I play them real cautious and fold a flush to big strength.
TR