Hi there,
My opinion on this one:
I just believe your not ranking well on the more competitive keywords for a few reasons:
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Your domain trust is very low because you only have 1 or 2 root domains linking to your website. That's not enough to start ranking well on more competitive keywords. Make sure to work on a strong link profile with more qualitative links (from different sources and root domains). This might be an interesting article to read.
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This remark relates to the previous one but make sure to provide quality content. Content where other websites can link to. You website looks more like a landing page at the moment.
As far as I'm concerned your certainly not penalized by Google.
Hope this helps,
Sander