If this is web connect I suspect the .qbo file is formatted the same as the last import. Confirm that this in fact is a new file and use the below instructions to re import.

How to re import web connect files

Reloading web connect files. Each transaction within the file contains a unique identifier. With a little manual manipulation you can modify this identifier and reload the file. However, be careful the purpose of this unique identifier to make sure you don't import duplicate entries.  

1. Open the web connect file with the text edit.   

2. Select edit>find>find and replace.  

3. In the search field enter <FITID>  

4. In replace field enter <FITID>1  

5. Select "Replace All", then done.  

6. Import the web connect file into quickbooks (file menu-> Utilities-> import->web connect)