I'd like to take a step back and ask how the previous systme performed in terms of cooling hte house. You said it was undersized, but you currently keep the upstairs and downstairs warmer than normal indoor design conditions.
I had a 3.5 ton system upstairs before and it struggled to keep it under 55%RH at night all last summer in hot and even more in mild weather. I downsized to a 2 ton and now it's under 50%RH without even going into "dehumidification mode" at all. This morning it was 78F outside and it was still 47%RH upstairs.
Could something be improved on your new system. Possibly. Anytime you change the equipment size, airflow and coil size, you'll change the dynamics of air distribution and humidity removal.
For all we know you ductwork was marginally sized for 2.5 tons and 1000CFM, now at 3 tons and 1200 CFM it's undersized so you have issues with even air distribution, so the downstairs is now getting more cool air.
How can we fix your problem? A competent contractor the really knows ductwork, equipment per formance and building envelope issues need to look at your home. A lot of these issues aer almsot improssible to diagnose and identify through a computer screen.
For example, maybe the new systm is depressurizing the basement more than before and now it's drawing in hot humid outside air through the sill plate, which on most homes unless it's carefully sealed, is very leaky.