Jake,
There are several options here.
I would suggest using your own code for datalogging. The datalogging you are referring to is primarily for debug, and one shot datalogs of front panel indicators (and controls?), not including graphs, etc.
If you go to the file functions, you will see a menu for datalogging. These functions will allow you to save your data, as you need it, simply, and in a compact format.
I recommend opening the datalog file, doing all your file operations, and closing the file before the program is complete. There are several examples of this in the examples database.
Good luck