The far-UV spectrum of the T Tauri stars (TTSs) provides important clues about the structure of the stellar atmospheres, winds and accretion shocks. The IUE (International Ultraviolet Explorer) Final Archive contains the most complete data base for such studies. A new extraction system, the IUE Newly Extracted Spectra (ines), has been developed to overcome the disadvantages of the extraction system used in the IUE Final Archive, the Signal Weighted Extraction Technique (swet). We have compared the ines spectra of the whole sample of TTSs in the far-UV range (1200-2000Å) with the swet low-resolution spectra available in the IUE Final Archive. Although in most of the cases there is a good agreement between both samples, an important enhancement of the ines line fluxes with respect to the swet line fluxes is reported for particular spectra. The line fluxes are enhanced by as much as a factor of ~2.5 in some objects, which is significant for variability studies of TTSs because the variations of the UV lines are typically of this order. The emission-measure distributions built to study the atmospheres of these stars are based on the UV emission line fluxes, so the new system is susceptible to introduce changes in these models. Moreover, the non-linear enhancement of the ines line fluxes produces variations in diagnostic line ratios usually taken as temperature and density tracers in late-type stars. These line ratios can vary by as much as a factor of 3 when the ines data are compared with the swet, with the subsequent variation of the physical parameters derived from them.