Possibly a bad panel. You've probably already discovered that there are holes or slots in the back of the fuses next to the amperage rating. You can use these holes to poke the multi meter probe into allowing you to take a reading without unplugging the fuse. You should get 0 volts from one slot to the other on the same fuse. On a single fuse, if you measure voltage from each slot to the ground you should get the same voltage. If you find a fuse where there is battery voltage on one slot but not the other slot that fuse is blown and needs to be replaced.
I would take a voltage reading on the battery itself and write it down. Next take a voltage reading on the battery wire at the fuse panel. The voltages should be the same or within about a tenth of a volt. Keep measuring voltage to ground further down the line (The slots on the reverse polarity fuses, the slots on the other fuses) until you find where the battery voltage drops significantly.