In previous investigations using the PTB Ion Counter nanodosimeter, significant deviations for large cluster sizes were found in the comparison between measured and simulated data of ionisation cluster size distributions. These deviations could be explained quantitatively using a simple parametric model for a background of secondary ions, which are produced within the transport system of the target gas ions to the ion detector. To correct for these secondary ions, unfolding procedures were applied to the measured data to remove the effects of this background. However, the parameters of the model describing the background of secondary ions strongly depend on operational parameters of the nanodosimeter, and any change in these operational parameters requires a new characterisation of the model's parameters. In this work, the influence of the nanodosimeter's operational parameters on the background of secondary ions and the collection efficiency of the detected ions was therefore systematically investigated. At the end of this process operational conditions were found where the background of secondary ions is reduced substantially while the effect on the spatial distribution of the collection efficiency is still acceptable. For some beam geometries of particular relevance for radiation biology, cluster size distributions measured with these new operational parameters can be used directly so that the unfolding procedures, and consequently the characterisation of the secondary ion background with respect to the parameters required by the corresponding model used in the unfolding, can be omitted.