If you really want .nomedia to do its job, follow these 3 steps :
• add a .nomedia to whichever folders you choose
• flush your photo gallery app's cache/data using your device's app mgr
• download/install a free media scanner app from the market (there are several) and invoke it … this last step will rebuild the photo gallery's cache/data… CORRECTLY this time !
Plus, you don't even need a rooted device for this : first step you can use any file mgr, even the dinky one that comes stock with Android devices, second step you can use your device's own app mgr as stated, and third step there are media scanner apps both for and without root, diff is only in some extra options, but invoking the Android media scan service itself is just one single line of code, no root needed.