This is based on following thread http://forum.piwik.org/read.php?2,99724
When importing log data, entries do not have the visitor ID passed from 1st party cookie. Detecting returning visitors is done via a sql lookup trying to match visitors in the past. Piwik only looks back visit_standard_length secnods by default. We could add a new config setting to force piwik to detect returning visitors better.
Clarified scope/ solution
Guess this one can be closed as window_look_back_for_visitor setting resolved the problem.
See FAQ: How do I improve Unique Visitors accuracy?