The correct behavior on startup is that D0, D1, D2, D3, and D4 should light up. So, it’s not that some of your LEDs are shifted, it’s just that one of them is not lighting up. Check the soldering at that LED location, and at the pins of the LED driver chips. Also make sure that that D1 is installed with the correct orientation.
Check the soldering at button “A” (aka location b1 on the circuit board) and the corresponding pin of the microcontroller, which is the pin located directly above the hole labeled PC1.
You may also want to download the Meggy Jr RGB schematic, to help figure out where to put the multimeter, if you want to do this that way: http://wiki.evilmadscience.com/Meggy_Jr_RGB
