Hey Pieter,
Another suggestion. If you are wanting to synchronize the analog inputs with the gps digital signal, an easy way to accomplish this would be to use the gps digital signal as an external clock for the analog input operations.
If you use a digital signal as an external clock, you will acquire one reading from the channel(s) in the scan list everytime the digital signal has a transition. This would create an easy way for the gps signal to set when you are actually reading data. Take a look at the LabVIEW shipping example 'Cont Acq&Graph Voltage-Ext Clk VI' that illustrates how to continuously acquire from analog input channel(s) using an external clock.
I hope this helps. Good luck with your application.
Regards,
Todd