Have you checked that SE got connected to the clock gaters cells correctly?
Is there actually a controllable path from the port scan_shift_enable to the clock gater enable cells? If not, that is the reason for the failure. You can check the controllablity of this path by using the dft_trace_back command:
Usage: dft_trace_back [-mode <integer>] [-polarity] [-continue] [-print] <pin|port>
trace back one level under the specified mode (0-3). 0: no constant propagation, 1:
tied-constant propagation, 2: tied-constant and test-mode propagation, 3: tied-constant,
test-mode and shift-enable propagation [default: 3]
also return whether the polarity changes through the trace
continue the trace back until PI, sequential gate, complex instance or constant is reached
print the status and pin at every trace back
pin or port to start the back-trace from
Use -mode 3 to propagate shift_enable.
You could also try temporarily using a primary input for SE (rather than using -hookup_pin) just to prove to yourself that controlling the clock gaters with SE is ok. But, I believe this to be a better solution than using scan_mode.