"When entered in the rollover section of the 1099-R screen for each of the IRA's 1099-Rs only one of them shows the amount NOT rolled over (taxable) on the return - the first one entered shows but the second one does not."

It's time to include more Details.

Example: An RMD typically has tax withheld. Did your client repay the gross amount by making up the missing Tax withholding, so that the rollover was in fact a Complete rollover of the RMD? And was that made by end of Aug?

Was the Second distribution from Trad IRA? Did it have withholding? Was it rolled over in the timeframe, and in full? Direct indirect?

See how all of that matters?