I always wait for 4 arc blast, then when it procs...missles. Not as good dps (on dummies) as 4 ablast then arc barrage and back to ablast. I have tried it every way and barrage is not as good dps. See, it's me. Wow hates me. lol
If you are hitting arcane missiles as soon as missile barrage procs, this could be the problem. You want to wait until you have 4 stacks from Arcane blast first. While stacking Arcane blast, if missile barrage procced somewhere along the way, then hit arcane missiles after you reach the 4th stack of Arcane Blast. If after 4 arcane blasts, you have no missile barrage proc, then you just keep hitting Arcane Blast until it does proc.