Is there a reason you're using a flipbook instead of an actual render out of your previous comp? That's a
very unorthodox use of one. (I didn't even know you could bring one in via Loader. Having tested it, I get the same result you do—Loop doesn't work.)
If you're intent upon using this workflow, you could use a TimeStretcher right after the Loader. Set the keyframes such that the clip plays properly—for a clip that should run from frames 1 - 30, set Source Time at frame 1 to 1 and Source Time and frame 30 to 30. Then go to the Spline View, select both keyframes, and click the Set Loop button.
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