Had something similiar to this before and discovered it was actually a data issue rather rather than anything to do with Qlikview. Can I suggest you get a look at the raw data and see if you can learn whats odd between missing data and included data. Wwe found the missing data was too many decimal places so we fixed the data.
Can I ask how you checked this data? Just throwing out that some tools might be using ODBC to connect to your data and it might still look the same. MS Access and Toad for me the data looked the same but SQL Query looked different. I'm know DBA but hoping the pointer might help.