How to measure Open Circuit Voltage of a Battery in Charging and Discharging state
You don't say what chemistry your battery is using. Different chemistries, lead, LiPo, NimH, have different behaviours in detail, but in general, the answer is, you cannot get an accurate SOC from the terminal voltage alone.

People are still doing PhDs on how to estimate SOC. I did some research into NimH for a commercial company recently and found that the history of the last hour charge/discharge affected the terminal voltage only SOC estimate at above the 20% level.

Your problem is not how to display the SOC, it's whether to 'fess up to the large uncertainties. The SOC will be essentially identical from one second to the next, even if you have switched from charge to discharge in that time, from pure physics reasoning alone. Your problem is the estimate you are getting from the IC changes under those conditions. 

You have several choices. 

1) Do more and better research on how to model SOC, and then implement the results of that. 'make it right'

2) Apply a low pass filter of several minutes to the results from your IC estimate, to disguise the step. 'hide it'

3) Figure out what the uncertainty in the estimate is, and then display your SOC as x% +/- y%. 'say what is'