Huh. I take it that the unregulated side is the one closest to the DC connector on the SB board?
That's NOT true of all the "freeduino" boards; the PCBs I did that are posted at freeduino.org, and are the basis of the nkc "freeduino" boards, have the 5V cap next to the connector. (basically, both unreg and 5V are present on both sides of the area where the caps live, so it's pretty much a whim which goes where.)
If you build one from a bare board, pay attention to whichever actual design you're using!