Yeah, since you mentioned earlier it only happened when the engine was running, it may be it was vibration related. Ie, something had been rubbing against a metal part that was part of the frame and thus grounded to negative; if a positive wire rubs through there and intermittently makes contact your fuse will pop (well, it's why there are fuses in the first place so that's a good thing).
So it may well be you'll have this issue crop up again if it was just some cable that got shifted a little during your troubleshooting, could even be something near the relay, you did pull it and wiggle stuff around in the process.