If there are any redstone sources near your hoppers, it may cause the hoppers to lock and will prevent the hoppers from transferring items. I'm not sure whether this is the case, but it might help.
Oh... whoops! Yeah, there was a redstone torch powering a powered rail, and also locking the hopper. However, I looked in F3 and it didn't say it was locked until I opened the GUI, so that is a bug. But yay, now it's not super loud!
If there are any redstone sources near your hoppers, it may cause the hoppers to lock and will prevent the hoppers from transferring items. I'm not sure whether this is the case, but it might help.