Source not found on debug only

(Reposting from coding questions as i got no answer there)

Very noob question but can you tell me why I keep getting "Source not found" when trying to debug a NIOS2 program for DE0 on Fedora?

It happens as soon as it hits a line that needs an include such as calling rand from stdlib.h

Sending it to the board works fine and I can light random LEDs, but I can't debug anything without commenting that stuff out which is daft.