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Random segment data not on reports

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About a week ago everything seemed fine, we are evaluating Piwik to see if it will work for our needs and are tracking 4M+ hits a day 5 sites total.

One site has 34 segments to break up the data for different sections of the site (www.blah.com/one/, www.blah.com/two/, www.blah.com/three/, etc) and all of a sudden random parts of random segments in the report just don't work. Some segments just don't have any data for random days, and when I go to pull up the segment statistics it tries to do a live query (which takes in the area of an hour just to query a day)

Does anyone have any idea why it may do this? I get no errors at all when importing or archiving data every day. I tried reimporting a month of data and that month still gets the same issue- random chunks of data just aren't there. For example it may have the segment data for November 15th for www.blah.com/one/ but not www.blah.com/two/, however it will have data for November 16th for www.blah.com/two/ and not www.blah.com/one/.

I am at my wits end trying to figure out what is wrong. Is it a MySQL limitation? is it PHP? I am getting no error codes at all from anything, I just look at my system and see MYSQL using up all kinds of resources when it looks for the missing segmentation data. and if I do a show processlist; query in the DB, it shows me it is churning away hard doing prepares and other queries.

I do daily reprocessing of my reports.

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