I think I disagree with your conclusion. On the face of it, the change from direct drive to chain drive should have increased the chances of a high cycle, bending fatigue failure. The chain is now a fixed side load on a rotating shaft. This causes a bending moment in the shaft that reverses with each rotation. You stated that the original direct drive arrangement was rigid. This throws up all sorts of red flags for me. I was always taught that you cannot put three rolling element bearings on a single shaft. It is impossible to perfectly align the three bearings. Any misalignment results in a bend in a rotating shaft, which is an ideal recipe for fatigue failure. You have never described the type of bearings. You never described the shaft location in terms of stress concentrations, keyways, steps, etc. Unfortunately, I also don't understand the machine this is driving. But allow me to theorize:
If the load from the machine was similar to an imbalance, it would rotate with the shaft and not produce a full reversal bending moment in the shaft. If the load from the machine is in a fixed direction and not rotating with the shaft, it could produce a full reversal bending moment. If the bearings are self-aligning (spherical bearings or a spherical mount within the housings) then the bearing would allow the bowed shaft to flex within the bearing. If the rigid mount of the motor on the outer side of the bearing prevented the bearing from flexing with the load, it could lock the bearing in place and the force from the fixed load would result in a high reverse bending moment adjacent to the bearing. Even with no fixed direction load from the machine, misalignment between the bearings in the motor and the pillow block bearings would produce the same affect. Changing to the chain drive removed both mechanisms, but introduced a new fixed load that could fatigue the shaft. But, apparently, this new load is not great enough to exceed the fatigue limit.
Vibration from the machine is unlikely to cause a shaft fracture. If it was a torsional vibration, it could break the shaft, but this was not a torsional failure. I didn’t notice any description of the vibration. A run-speed vibration indicative of imbalance should not fatigue the shaft. A two-times run-speed vibration indicative of misalignment could indicate a bending condition that might fatigue the shaft.
In the end, the answer is the same. Reduce reverse bending moments in the rotating shaft. Reduce stress concentrations at high stress areas of the shaft. Use a material with good fatigue properties, less brittle, not as notch-sensitive. It sounds like you accomplished a couple of these changes, but not all of them.
You did not do a very good job of describing the problem. You did not do a very good job of providing the available data about the machine design or vibration. Without much detail to go on, our answers tend to break down into speculation and result in frustration (as you saw on the other forum where you posted this same issue). Add double posting into the mix and you may not make many friends.
Johnny Pellin