Did your vet test the live ones and the dead ones for BVD or IBR? Start there get them tested. Sounds like you got a bunch of PI calves.
Did you booster your animals when required? This is important as well.
Some vaccines that have say, homophilis (sp) really need to be boostered. They all do infact
Did you use a modified live or a killed vaccine?
A modified live (ML) has a tendancy to get a PI animal sicker and insight death quicker. If these calves are PI calves, the vaccine will not help because they are already sick.
If an animal is a PI (persistantly infected) animal, stresses can be weather changes, feed changes, mineral problems, handling stresses can exasperate the problem and they get sick and die.
The basics of a PI calf are:
The mother was infected with BVD sometime during gestation. The mother (dam) was not protected by being vaccinated. The disease passed through the placenta infecting the calf. The calf is born weak, and gets sick easier. Scours, pnemonia etc. Most PI calves have a short life span, and can die at a drop of a hat, get sick just by looking at them wrong...so to speak...you get my point.
Poorly timed an poor quality colostrum at birth can have a serious affect on this as well.
The problem with PI calves is they shed the virus all the time through every opening of their body. So this raises the virus threshold in the area the animals are kept. If a calf is stressed, and if the threshold is beyond what they can handle, you will see alot of sickness and deaths.
The trick to prevent things like this are
Buy preconditioned calves
Buy from reputatable farmers
Buy from farmers who vaccinate the cows and bulls a minimum of 3 weeks prior to breeding and are on a good herd health program
Start testing for BVD and IBR, homophilis, etc...dead and alive