Using GPIO in Altera
Most likely the problem is the pins assignment, make sure they are assigned correctly.
Posting the pin assignment here might help us find the problem.

Anyway, Please test it without a clock and let us know.

module gpio_test (CLOCK_50, GPIO_0, LEDG);
input   CLOCK_50;
input   [35:0]  GPIO_0;
output  [7:0]   LEDG;

assign LEDG[0] = GPIO_0[0];

endmodule