What fields did you map for your contacts CSV? This is likely due to either the default settings or provided values for the assignedTo and visibility fields. If visibility is set to "Private" (0 in the db), and the contact is assigned to "Anyone", the record will be hidden from grids. This is the mechanism used by the duplicate checker to hide duplicates. You'll want to ensure that visibility is either Public or User's Groups (1 or 2 in the db), or that if the record is private that it is assigned to a user or group. If you've customized the default values for these fields, you may want to verify that they do not hide records when they are created without a provided visibility and assignedTo. The new 6.6 release includes a "Find Missing Records" admin tool to help users locate records which may have been hidden in this manner.