Trouble configuring Virtex-5 FPGA using JTAG

I'm trying to configure a Virtex-5 FPGA on a custom board and I'm using Xil inx iMPACT in order to program the FPGA using a JTAG interface. But iMPACT has trouble detecting the FPGA and gives an error about not being able to d etect the FPGA even though it is powered on. I tried to program a similar b oard and I was able to do so without any issues. The board designed is a cu stom board so I'm wondering if there is something going wrong on the board itself or if it is a problem with the JTAG configuration. I use two differe nt cables for the different boards so I'm not really sure where the problem lies.

I probed the JTAG signals on both the boards to see if the waveforms are co rrect and it looks like the waveforms are way off.

I've given links to the schematics of the two different boards and their re spective waveforms and it looks like there is something wrong with the cust om board.

Schematics : The schematics are only for the JTAG configuration

Evaluation Board :

Custom Board :

Waveforms : The waveforms are when I use the Initiate Chain command from iM PACT

Evaluation Board :

Custom Board :

I'm not sure if there is something wrong with the JTAG cable itself or if t here is something else that is wrong with the fpga power etc.