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FCAL_EN is not necessarily issued
https://github.com/Xilinx/embeddedsw/blob/8fca1ac929453ba06613b5417141483b4c2d8cf3/XilinxProcessorIPLib/drivers/rfdc/examples/xrfdc_clk.c#L514
This code that should issue a FCAL_EN command is not quite right per the documentation for the LMX2594, something like:
tx_array[2] = (unsigned char) ((r[112]) & (0xFF)) | (1 << 3));
would ensure this rather than rewriting R0 with whatever value was in place