Prototype long pulse ion sources are being developed and tested toward the goal of a deuterium beam extraction of 120 keV/65 A. The latest prototype source consists of a magnetic bucket plasma generator and a four-grid copper accelerator system with multicircular apertures of 568 holes. To measure the angular divergence and the ion species of the ion beam, an optical multichannel analyzer (OMA) system for a Doppler-shifted H-alpha lights was set up at the end of a gas-cell neutralizer. But the OMA data are very difficult to analyze due to a large background level on the top of the three energy peaks (coming from H(+), H(2) (+), and H(3) (+)). These background spectra in the OMA signals seem to result from partially accelerated ion beams in the accelerator. Extracted ions could undergo a premature charge exchange as the accelerator column tends to have a high hydrogen partial pressure from the unused gas from the plasma generator, resulting in a continuous background of partially accelerated beam particles at the accelerator exit. This effect is calculated by accounting for all the possible atomic collision processes and numerically summing up three ion species across the accelerator column. The collection of all the atomic reaction cross sections and the numerical summing up will be presented. The result considerably depends on the background pressure and the ion beam species ratio (H(+), H(2) (+), and H(3) (+)). This effect constitutes more than 20% of the whole particle distribution. And the energy distribution of those suffering from collisions is broad and shows a broad maximum in the vicinity of the half and the third energy region.