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I've had the exact same experience and have been trying to figure out why ever since. Others here have discussed the same problem. In my case it may be because Google seems to be giving more credit to root level index pages but that doesn't explain it all. I think we are just going to have to wait until all these changes are done on Google and see if it sorts itself out.
Meanwhile concentrate on getting your content pages up. Content pages can bring in a great many visitors and usually involve more specific, less competitive search terms.
during this update or whatever I had the experience of not finding my index page for what was on page just for anchor text and title, this did change though. Either something was wrong with the way I searched or the way google searches had changed.
I am not taking anything seriously just now.
IŽ ve been around all these days about this subject and I have some conclusions:
www.mysite.com not show in the results after freshbot is in index results (some short of penalization occurs), main page retourn to the former positions when freshbot results vanish, so for that people having beat by fressy every day this last may not occur.
I am the owner of 4 domains very well targeted in different but related areas, Top one has this problem (the site is updated every two days and the main kw has hight density on page) the other three are more statics and due to they are only optimized for Title and url maybe they are not "penalized" for over-optimization, the funtion seems to have a maximun and if you overpass that maximun you rank lower, nothing to do with PR (my PR still the same) is just a filter, or may be the other sites are more statics and fressy do not visit so frecuently (i really do not belive this last one to much), unfortunately i do not have logs for those static domains.
So my static domains with no Kw1-Kw2 on text, just one Kw1-Kw2 on title and url are performing well and stable, the other one more dinamic, more optimized in the main page is not showing in index in good positions after freshbot results are in index and it is show after my fresbotted pages disapear.
I was #1 for the main Kw of the four domains.
I think there is nothing you can do right now, maybe G is using your optimized pages to check their filters and no final threashold is stablish yet, or if it is stablish may change in the future very often.
Problem appart is the backlink count, and the three months cached pages (the results when freshbot index results dissapear are based on the three or two moths ago cached pages)
Sit, wait and relax.
[edited by: Ataulfo at 10:44 pm (utc) on May 30, 2003]
Freshbot picked it back up and now lead the SERPS again for this obscure phrase. I banned Google from my forum in hopes that it no longer gets "lost" and misplaces my pages!
Jim