Google Penalty from PHP Link redirect?!

I am 100% out of ideas as to why my site is penalized in google... It's been like this for almost a year.... 1 day it will have great rankings, then it isn't in top 1000 for months...... then it comes back and goes away after a few hours.......gone again for months...

Here's where it stands:

1. ranks SUBPAGES, not homepage #2 and #3 for the site name. ("mysite")
2. Most pages don't even rank in top 100 for their full title tag.
3. 107 indexed pages (yep that's all of them so that's good)
4. backlinks showing
5. No penalty alert in webmaster tools
6. Using sitemaps, checking out fine.
7. Google shows all my backlinks in webmaster tools
8. Homepage has Pr1, one subpage has pr3 (wtf), and another subpage has pr1.

I don't do any shitty link stuff like exchanges. It's all natural in-content 100% relevant and very carefully done natural linking. I also run a quality site with tons of content. It's not a "thin affiliate site" that's for sure.

I have ONE last idea...... Could Google have penalized my site for using php redirects for my affiliate links? like....

mysite.com/visit.php?id=afflink1

 

that may be the reason

but whether you bought any paid sitewide links?

 

I have not bought any sitewide links, thanks

 

Sounds like need to work on links and content more. Doesn't look like a penalty.

 

1. ranks SUBPAGES, not homepage #2 and #3 for the site name. ("mysite")

- This is because your internal web pages apparently have better backlinks and on-page optimization. This is far from uncommon, your goal should be to get internal web pages to rank for a variety of keywords.

2. Most pages don't even rank in top 100 for their full title tag.

- You need to build relevant backlinks to your web pages, using as anchor text the keyword or keyword phrase your trying to rank for.

8. Homepage has Pr1, one subpage has pr3 (wtf)

- Again, that web page has more backlinks of quality or quanitity.