I was the lucky recipient of a stress fracture in my 2nd metatarsal during high school. I was a mile into a race when it happened. I absolutely knew something was wrong when it happened, even though I was able to finish. I couldn't walk correctly for a few weeks. I was off from running for like two months.
As with any running injury, if all you do is take time off and then go back out and start running, well, you've really done nothing to prevent it from continuing to happen. Time off gives the body a natural opportunity to heal, but does nothing to address what you may be doing to cause it.
The causes of metatarsal pain are typically something that makes your foot bend in the metatarsal area. I don't want to point a definite finger here, but shoes like the Brooks Glycerin or Launch with the sprung toe are the sort of bending that can lead to metatarsal issues.
((I think in my case it was a weird combination of suddenly doing a lot of jump roping that strained my metatarsals, which then went overboard when I put on spikes and ran a cross country race.))
Also, running off the tips of your toes can also cause a lot of pressure on the metatarsals. Speedwork, extremely flexible shoes, or odd mechanics can cause that.
It's worth noting that I also expect some stability features on shoes can cause it. Perhaps it would be more accurate to say arch support can cause it. Having something built up under your arch can create a sort of transitional valley under the balls of your feet, where the arch is pushed up, the balls of your feet land down in the normal insole area, and then you push off with your bent up toes. That's a ton of pressure on the metatarsals.
I'm rambling on, but the point is that it's entirely possible you took time off and then went outside running doing the exact same thing that was causing the metatarsal pain to show symptoms. It's hard to say whether that type of running caused the symptoms or is just bringing them to light. Good luck with figuring that one out.