Fact 1: the websites kicked are part of a network with multiple sites crosslinked.
Fact 2: some webmasters use multiple servers so its not only the IP's
Fact 3: before allegra all sites did rank well.
Fact 4: the stronger site of the network did take place in the ranks from the kicked one, not always as high...but visible.
Fact 5: the kicked sites have not enough links else to gain authority.
Conclusion:
With the previous IP matter i have a mixed feeling now because seeing the results from others i think it is a factor but less then the linkstructure.
This does not take away the advice that if you have multiple sites its better to spread them on different servers.
In all cases i see that there are 3 or more sites directly involved in this link network and that there is not enough link or domain popularity from other sources to balance these links.
A part of the google secret was revealed when i was looking at the related sites some time ago. I did see that google does count also more sites as related if they link to one site in your network, also when there is no direct path to it. (has to pass through multiple sites)
Now that we see that certain linkstructures are not the best solutions it's my advice to remove those links in your network.
To my opinion the best way to link is like islands because the whole internet is build like this. You should be carefull with setting things up and make the circle of coming back to a certain site as far as possible.
Because an image says more then words i have created an image file which can be seen here.