SUMMARY Global positioning system (GPS) position time-series generated using inconsistent satellite products should be aligned to a secular Terrestrial Reference Frame by Helmert transformation. However, unmodelled non-linear variations in station positions can alias into transformation parameters. Based on 17 yr of position time-series of 112 stations produced by precise point positioning (PPP), we investigated the impact of network configuration and scale factor on long-term time-series processing. Relative to the uniform network, the uneven network can introduce a discrepancy of 0.7–1.1 mm, 21.3–27.5 μas and 1.3 mm in terms of root mean square (RMS) for the translation, rotation and scale factor (if estimated), respectively, no matter whether the scale factor is estimated. The RMS of vertical annual amplitude differences caused by such network effect reaches 0.5–0.6 mm. Whether estimating the scale factor mostly affects the Z-translation and vertical annual amplitude, leading to a difference of 1.3 mm when the uneven network is used. Meanwhile, the annual amplitude differences caused by the scale factor present different geographic location dependences over the north, east and up components. The seasonal signals derived from the transformation using the uniform network and without estimating scale factor have better consistency with surface mass loadings with more than 41 per cent of the vertical annual variations explained. Simulation studies show that 40–50 per cent of the annual signals in the scale factor can be explained by the aliasing of surface mass loadings. Another finding is that GPS draconitic errors in station positions can also alias into transformation parameters, while different transformation strategies have limited influence on identifying the draconitic errors. We suggest that the uniform network should be used and the scale factor should not be estimated in Helmert transformation. It is also suggested to perform frame alignment on PPP time-series, even though the used satellite products belong to a consistent reference frame, as the origin of PPP positions inherited from satellite orbits and clocks is not so stable during a long period. With Helmert transformation, the seasonal variations would better agree with surface mass loadings, and noise level of time-series is reduced.