Well, your code is not reproducible so we will never know for sure, but this is what help('break')says:
break breaks out of a for, while or repeat loop; control is transferred to the first statement outside the inner-most loop.
So yes, break only breaks the current loop. You can also see it in action with e.g.:
for (i in 1:10)
{
for (j in 1:10)
{
for (k in 1:10)
{
cat(i," ",j," ",k,"\n")
if (k ==5) break
}
}
}