I'm having a problem with u-boot 2016.01 failing to detect the FPGA on my Altera Cyclone V SoC Development Kit. On startup, it simply prints "FPGA: Not Altera chip ID" (the ID having been read as all-zero). No amount of messing with jumpers or switches makes a difference. The software on the SD card included in the box appears to work, so on a whim I took the SPL pre-loader from this card and combined it with the main 2016.01 u-boot. This makes the detection succeed, despite Marek baulking at this idea. The "good" SPL identifies as "U-Boot SPL 2013.01.01 (Dec 04 2014 - 08:59:41)" which is a different build date than the main u-boot on the same SD card, so which source code version it was built from is anyone's guess.
What's interesting is that Marek's board works with u-boot 2016.01 while mine fails even with the very same binary. The boards are different revisions (his 100-0321003-C1, mine -E1), and the main Cyclone V chips are also different (his 5CSXFC6D6F31C8NES, mine 5CSXFC6D6F31C6N).
Any suggestions for what to try next?