Soft lags from the emission of the lower kilohertz quasi-periodic oscillations (kHz QPOs) of neutron star low mass X-ray binaries have been reported from 4U1608-522 and 4U1636-536. Those lags hold prospects for constraining the origin of the QPO emission. In this paper, we investigate the spectral-timing properties of both the lower and upper kHz QPOs from the neutron star binary 4U1728-34, using the entire Rossi Xray Timing Explorer archive on this source. We show that the lag-energy spectra of the two QPOs are systematically different: while the lower kHz QPO shows soft lags, the upper kHz QPO shows either a flat lag-energy spectrum or hard variations lagging softer variations. This suggests two different QPO-generation mechanisms. We also performed the first spectral deconvolution of the covariance spectra of both kHz QPOs. The QPO spectra are consistent with Comptonized blackbody emission, similar to the one found in the time-averaged spectrum, but with a higher seed-photon temperature, suggesting that a more compact inner region of the Comptonization layer (boundary/spreading layer, corona) is responsible for the QPO emission. Considering our results together with other recent findings, this leads us to the hypothesis that the lower kHz QPO signal is generated by coherent oscillations of the compact boundary layer region itself. The upper kHz QPO signal may then be linked to less-coherent accretion-rate variations produced in the inner accretion disk, being detected when they reach the boundary layer.