FlexLogger features a Plugin Development Kit that you can download at the following location:
FlexLogger Plugin Development Kit Download - NI
Using this kit, you can create FlexLogger plugins to acquire data from 3rd party devices.
You create those using LabVIEW, and LabVIEW has the capability to call DLLs. In your case, you will need to interface with the Arduino API DLL.
For your reference here is a link to the online documentation:
FlexLogger Plugin Development Kit API Reference - NI
Hope this helps.
Principal Software Engineer, FlexLogger.
Have a look at the LINX toolkit (download, forum) for letting LabVIEW VIs talk to an Arduino. A FlexLogger plugin written in LabVIEW would need to call the LINX functions to establish serial comms to the Arduino, poll the I/O, clean-up serial comms, etc. The arduino data would then be read by FlexLogger for display and logging.
Note that writing a FlexLogger plugin requires LabVIEW, but once it's compiled it can be deployed to a system that only has FlexLogger installed.