The AD-FMComms5 (AD9361) assumes a VDD_INTERFACE voltage between 1.71V and 2.625V (1.8 to 2.5 +/- 5%), so on your FPGA carrier board, you should ensure that VADJ is between these levels. Setting things to 3.3V will damage the part.
Traces between baluns and SMAs are not phase-matched on REV-A and REV-B which can cause phase misalignment with the libad9361-iio ad9361_fmcomms5_phase_sync solution. This is corrected on REV-C. Therefore, phase alignment performance can vary over frequency. The RF switches on REV-A/B are also not designed to work above 900 MHz. Higher frequency switches are available on REV-C.
Below are some preliminary results using Release 2018-R1 with equal length but unmatched cables