Are you using the 'Count Buffered Edges VI'? I have tried it out and have not had any problems with it with a 660x board.
There are two parameters to set, 'counts to read' and 'time limit'.
The 'counts to read' parameter sets up how many values to read from the counter at a time. If, for example, you want to know the counter value for every pulse on the Gate, you would set this to one. However, for faster Gate frequencies, it is helpfull to set this high.
By default it is set at 100, due to this, it will read 100 counts at a time.
The 'time limit' parameter sets how long to wait for 'counts to read' number of counts. If you set the time limit to 10 seconds, though you don't get 'counts to read' number of counts, it will just return however many
counts it does have.
Let me know if this does not make since or you are seeing different behavior.
Brian