I know it's an old post, but just though I'd contribute.
I'm not sure, but it seems your problem is that you don't feel comfertable with your picking hand. Without being used to picking any string in any way at any time, doing scales will require you to keep you're attention on bothhands. This is extremely difficult. Your picking hand needs to be trained well enough that you can pick dead notes on random strings in random patterns while talking to someone.
When I started I put my hand over all the strings and muted them. Just rest your fretting hand on the strings. Then I went through a series of exercises (I think it was Alexi Sklaverskis slap practice, but I did it with my fingers alternating all the time). Without the problem of which notes I'll hit I could focus on my two fingers. These exercises were very elaborate:
First it was picking each string 4 times, of course done with a metronome (or in my case, a drum loop on the PC) to get the timing perfect.
Second it was two picks on E and then two picks on A, repeat and then move on to other strings.
The third part was one pick on E and on A, repeat and move on to other strings.
Later it got more challanging like picking E and D alternatively and so on.
This is actualy a thumb precision exercise, but it helps a lot to get the fingers moving for a beginner. Once you got the hang of these, start doing scales and you'll notice that your hand will move on it's own and follow your freting hand without you even thinking about it.