I was seeing this issue with certain data using the latest Telerik DLLs as of October 2014, and found that sorting any column would cause the row alignment to be corrected, so I implemented this fix:
// Sometimes the pivot grid row becomes misaligned with the other rows, but lines up after applying a sort.
// This will force a sort on page load (but in default sort order so the action isn't apparent) to fix the problem.
pivotGrid = $find(
'<%= RadPivotGrid1.ClientID %>'