The problem is that the SYNC signal is not receiving properly.
After initialization by writing 0x401, 0x400, 0x088 and 0x482 to the register, the SYNC signal is fixed to high state as shown below.
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Hi there!
Welcome to our e2e Forum! There are some things you have to keep in mind with the THS1209 - first is that it is a pipeline converter, this means you need to apply the CONV_CLK to get conversions started through the pipeline before you see the first SYNC output. This is described under SYNC on page 14 of the datasheet. Once you get the first SYNC, you need to apply your /CS0, CS1 and /RD in the same manor depicted in Figure 26. If you don't apply the /RD with every clock cycle, you can get some strange behavior from the SYNC output. In the screen shot you provided, you should have started reading data (at least) three/four cycles earlier than what you have shown.