I'm mining a tunnel and have a setup where I have a minecart with a chest that I can fill up at the end of the tunnel, send it off, it unloads by itself into a large chest (using a funnel and a redstone setup) and then it comes back by itself. For some reason, the minecart and chest isn't coming back anymore. If I send the chest and then follow behind it with a minecart, everything works fine. On the other hand, if I send it off by itself and continue mining, it doesn't come back (even after 15 minutes, while it should take 1). I go see why using a minecart and I see it come back in my direction.
My guess is that it was working fine for you, but you started mining further and further away from the unloading station, to the point where the unloading station was in a chunk that is no longer staying loaded.
Another reason could possibly be due to the amount of materials inside the chest. As the chest has more spaces filled up, it's speed goes down significantly. If your system of powered rails (or whatever way you propel it) doesn't provide enough power or is spaced out too far, then the cart may just be getting stranded on the rails. It wouldn't hurt to check and follow its journey either.