You are overthinking this aspect. At this stage of your lifting, you don't need to necessarily "target" a muscle. A heavier exercise (done with proper form of course) will make you stronger. Focus on getting stronger overall. That's the whole basis of the Starting Strength routine. Which brings me to my next point...
You obviously weren't training long enough. How long did you try Starting Strength? Did you follow it as it was written, or did you change things (i.e leg press instead of squat, not adding weight for the next workout if you acheived all 3 sets of 5, etc.)? By your previous statement, I'm willing to bet you haven't really been pushing yourself by adding weight when you should have been.
Also, you stated you have the nutriton down and are eating enough. Are you sure about this? Most people who state that they are "eating enough" yet aren't noticing gains are actually NOT eating properly.