Every time I log in, I have to drag my secondaries out into the tool bar. I am a fire/healing blaster.

I have a toon with the same power set and I have the same problem, I reported the bug in game I don't know if anyone else is having this problem with other builds.

agreed, the secondary power on two new character never appears but I can drag it out.

I can also make copies and copies of powers, but not sure how to remove them

I remove the copies by right clicking, which brings up the option to clear.