What do you mean by "under designed by 40%"? Can you elaborate a bit? Are the failures happening in uplift checks or gravity checks? Flexural or axial failure? Or both? Or just when combined? What are your boundary conditions for the analysis? Give a little more of that kind of detail, and somebody may be able to identify a likely input error.
Analyzing these things can be a bit tricky - I've only had to dig that deep into them a few times, and it took some "massaging" of the calculation to get everything to make sense.
Do you know when the building was built? If so, make sure you grab the SJI spec from that time period (currently published in the 75 Year Joist Manual, I think I have a copy of the 60 Year Manual). As retired13 says, they have their own method. There are standardized calculations to determine allowable stresses based on joist geometry. That could help shed some light on how they would have originally designed it.