Crosslinked sites treated as the same site by google

Hello,
Some partners and I noticed something in google's behavior which is not very well covered (saw some evidence of it in forums but nothing black or white).

We all have networks of over 50 sites interlinked in some way.
1. My network is separated in groups of 20 sites (similar niches) all interlinked from the index page, same host but diffrent C class;
2. One of my partners is interlinking in groups of 5;

I have been hit by penguin while my partner didn't - I must have tripped a cross linking scheme penalty having 20 sites interlinked (each with another); my partner, crossing just groups of 5 seemed to stay under the threshold.

What we have observed, regardless of the penalty I was talking about:

When you have a network interlinked, google treats the whole network like the same site.

There are many reasons to suspect this:

1. Some sites which have good serps and have no major changes drop exactly when other sites in the network rise in serps.

2. Often when you have a network you can't build links constantly on all sites, so google maybe thinks that the sites with fresh links are the highligh of the network and gives them great serps, dropping the older, less updated sites.

3. I know guys who have thousands of interlinked sites on the same niche - if google would give all the sites good serps they would dominate the index and I think this is what google does, tries to give everyone a piece of the pie.

Has anyone noticed this also?