problem of configuring two different FPGAs

[Altera_Forum]

My board has two FPGAs (both EP3C16E144I7) designed to be programmed with Active Serial and JTAG. It is working fine. I can program the two FPGAs through JTAG with sof and jic, or through AS flash interface with pof. 

 On a new release of the board, the first FPGA in the JTAG chain is changed to a bigger device (EP3C40F484C8). Everything else remains the same. Now the JTAG chain cannot be detected reliably by "Auto Detect" in Quartus Programmer. Sometimes it succeeds, sometimes it fails. And if I try to program with sof, jic or pof, it always fails.  Could anybody give me a hint of this? Is there anything I need to pay attention to when putting two different FPGAs in a JTAG chain?  Attached photos show the waveforms of JTAG TCK and TDI of the old good board, of the new board when it passes Auto Detect, and of the new board when it fails Auto Detect after clicking "Auto Detect" in Quartus Programmer.   Thank you very much!

[Altera_Forum]

There is no problem when mixing FPGAs. I regularly have JTAG chains with MAX II devices and Stratix devices. My new board will mix MAX II, Cyclone IV, and Stratix IV. 

 The main thing you have to be careful of is buffering TCK/TMS so that each FPGA gets its own copy.  Zoom in to the JTAG TCK waveform very closely and see if the edges are monotonic, with no dips.  Cheers, Dave