Like you have said, and others have tried, running a 3V3 signal into the cRIO will not trigger a logic high for the cRIO. You must use some type of logic level converter(LLC) to perform the task you are desiring. (3V3-->5V)
Picking the proper LLC depends on the frequency of switching that your application requires as well as the type of signal you are running (i.e is it bidirectional or not). However, without knowing this, I can at least point you in the right direction to start looking...
Sparkfun Electronics sells a cheap LLC board that is run off of the BSS138 Transistor. It should work for you, and has worked for other teams
Link to Board
Link to Schematic
Link to Transistor Datasheet
Also, here is a relevant thread from last year:
http://www.chiefdelphi.com/forums/sh...d.php?t=101407