Is there live load reduction being used in the design combo for example based on the design options you have chosen?
Create design combos that compare only constituent loads, i.e. isolate the gravity & isolate the live load into single cases, determine where the difference in deflection is occurring, is it in dead or live or both.
Which if any is correct based on a hand calculation, or using alternative software, you didn't say? Satisfy yourslef that the design output is relative to the beam ends as per the analysis window, etc.
Review the line loads in each case that tribute to the beams under display loads, perhaps one case is accounting for the self weight of the member and the other isn't.
Are there any errors in the analysis log?
You have not really explained what you have done to at least eliminate some possibilities?
CSI are usually quite helpful in taking a look, at the end of the day the discrepancy could simply be a program error. Their programs seem prone to them, especially in new versions (just check the change logs for example to see the varied bugs that get fixed, many which have been around for multiple versions of the program!).