The Taiwan photon source (TPS) is a 3 GeV synchrotron light source now in routine operation at the NSRRC. At the beginning of beam commissioning, significant photon flux dips could be observed at injection due to a blow-up of the beam size. To eliminate this transient effect, all four kickers were rematched. The leakage field was shielded and the induced current loops at vacuum chambers in the injection area were also eliminated. These efforts reduced the horizontal betatron oscillations and orbit distortions to around one-tenth. In order to decrease the recovery time of photon dips during injection, the operational chromaticity was reduced to improve incoherent effects. After all those improvements, the photon flux dips during injection dropped to 30 % and the recovery time to less than 1 msec.