Odd wiring setup with switches - causing problems with light fixtures

When I moved into my house three years ago, there was a digital timer switch installed by the front door, as well another switch that works as a 3-way for the foyer light. I've been having issues with the digital timer recently, where it will stop working, so I figured it's starting to go, so I bought another one, but very confused when looking at the wiring that was done. House is about 10 years old. Current switch box holds 3 switches, one is a 3-way, 2nd is a switch for lights outside the garage and 3rd is for lights outside the front door, however the wires for the garage and front door lights were tied together, then tied into the digital timer switch -- so there is a blank switch plate in the middle of the two switches. The worst part is all the wires are BLACK, except for ground wires. The one wire, connected to the bottom of the 3-way switch, is tied together to two separate wires that come in from the top of the box, which then has a jumper connected and leads to the digital switch.