Cyclone IV E: EP4CE22F17C8 I/O pins misbehaving

This is using a custom PCB.

For testing purposes, I drive pins A11 and A13 with a 1MHz clock signal generated by the Quartus PLL IP block. Using an oscilloscope I probe the pins, and I can see the 1MHz waveform output from A13, however, the output form A11 is a constant high signal.

Pin L15 is the MISO to a peripheral ADC. For Pin L14 I use logic and assignments which have worked on a previous device. Moreover I have an identical interface elsewhere in this project which behaves as expected. Using the oscilloscope I can see that Pin M7 is able to be controlled by the peripheral chip. Pin L14 should behave the same but is being held high the entire time.

module ad7276(
input clk, //PLL clock 48MHz
input rstn, //PLL Lock signal
input shdn_ext, //Hardware wire OR'd laser shutdown

output reg SCK, //ADC SCK 24MHz
output reg SCSn, //ADC CS
input MISO, //ADC Master-IN Slave-OUT

output reg [11:0] MEAS, // Measurement
output reg meas_rdy
);

reg [5:0] count; // [0-13] Tconv, [14] Tacq, (b0 & b13 read 0)//0-26 Tconv, 27-28 Tacq
reg [11:0]dummy_meas;
reg SCSn_d;

always @(posedge clk)
begin
if(!rstn || (count == 38))
count <= 0;
else
count <= count + 1'b1;
end

always @(posedge clk)
begin
if(!rstn)
begin
SCK <= 0;
SCSn <= 1;
end
else if((count <= 2) || (count >= 37))
begin
SCK <= 1;
SCSn <= SCSn_d;
end
else
begin
SCSn <= SCSn_d;
SCK <= !SCK;
end
end

//CS low except during acquisition (2 clock cycles @ 48MHz)
always @(posedge clk)
begin
if(count == 38)
SCSn_d <= 0;
else if(count >= 38) //was 35. wasn't getting above 1.5V on o-scope TP
meas_rdy <= 0;
else if(count >= 34)
begin
SCSn_d <= 1;
MEAS <= dummy_meas[11:0];
meas_rdy <= 1;
end
else
begin
SCSn_d <= 0;
meas_rdy <= 0;
end
end

//Clock data_in with SCK when count = 6-28 and CS is low //deserialize miso
always @(posedge SCK)
begin
if(count >= 6 && count <= 28 && !SCSn)
begin
dummy_meas[13-((count/2)-1)] <= MISO;
end
end

endmodule