You are doing something wrong but not sure what. The most complete schedule will be Trenitalia.com. The Italotreno.com is a private railroad company using/leasing Trenitalia tracks and stations. Their schedule is primarily high speed trains between major cities. Either is good choice. It is my understanding the italiarail is a travel agency selling railroad tickets. Stick to Trenitalia first and treno second. Give me one of your routes, day and time, and I will see what I can find.
There are several levels of trains -- the high speed that make travel faster between cities and don't go everywhere. Intercity, Intercity Expresses, a little slower and makes more stops. The Regionale trains (think - bus on wheels) is the slowest, most stops, cheapest, and go almost everywhere. A quick check shows the faster train with one change is 2 hours and some minutes. The Regionale trains take five hours and a couple of changes.