New measurements of the reduced cross section $sigma_r^{D(3)}$ for the diffractive process $ep to eXY$ in the kinematic domain $12 leq Q^2 leq 90$ GeV$^2$, $0.01 leq beta leq 0.65$ and $xpom<0.1$ are presented. Data events recorded by the H1 detector during the years 1999--2000 and 2004 have been used, corresponding to a total integrated luminosity of 68 pb$^{-1}$. The measurements are derived in the same range as previous H1 data, namely $M_Y < 1.6$ GeV and $|t| < 1.0$ GeV$^2$. Two different analysis methods, rapidity gap and $M_X$, are used and similar results are obtained in the kinematic domain of overlap. Finally, together with previous data, the diffractive structure function measurements are analysed with a model based on the dipole formulation of diffractive scattering. It is found to give a very good description of the data over the whole kinematic range.
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