There is a bug in U-Boot 2017.09 in the fdt set command, which prevents it from being able to add a property to a device tree node. That version is the default in buildroot-2017.11-rc2. U-Boot 2017.11 is now the current release. I haven't yet confirmed if the bug is fixed in 2017.11.
The bug affecting fdt set is still in uBoot 2017.11, so there is no reason to consider changing the default in buildroot on that account. The bug is not present in uBoot 2017.03.
I'm not sure which exact problem you had. However, it really seems like a problem in upstream U-Boot, so you should report this to the U-Boot developers instead.