I assume you are quoting percentage errors in estimates of g.
The SHM approximation takes the restoring force as proportional to θ, whereas in reality it is proprtional to sin θ. So for the large angle you are using, the restoring force is overestimated. This will lead to an underestimate of g, probably by a constant factor. This could explain the errors at the longer pendulum lengths.
This suggests another source of error which tends to overestimate g more at the shorter lengths.
Of course, if you are quoting percentage errors in the expected periods, that all gets turned on its head.