So you're booting the HPS and having it program the FPGA (HPS boot first flow) which includes Signal Tap.
Then when you try to access the Signal Tap instance in the .stp file, you are not getting a status of "Ready to acquire" even though the device shows up in the JTAG Chain Configuration section of the window? The tool does not require you to manually program the device. As long as the device is programmed with a design that includes a Signal Tap instance (and your .stp file settings are compatible with that instance), it should work over JTAG.
As a test, I'd try manually programming just the programming file to the FPGA (not booting the HPS) and verifying that Signal Tap works that way. If it does, can you verify that the HPS is successfully configuring the FPGA itself with the same image?