Unless the existing refrigerant is compromised by the mixing other refrigerants as Capz suggests, the system performance won't be significantly improved by switching to another R12 interim replacement refrigerant like R414B or R401A. There's nothing inherently bad about R409A.
I think we need to get back to some basics first...like doing a quick load calc for the box and comparing that to the expected capacity of the existing system.
What is the size of the box?
What is are the model numbers of the condensing unit and evaporator?
If the load and capacity appears to be in line, then perhaps checking the compressor performance would tell a tale. Get the suction and discharge pressures along with the amp draw and input voltage at that condition. With that info, we can go to the compressor manufacturer's performance data and determine what the amperage should be.