That surprises me. Since that's the case, you might consider an alternate matrix representation. Is it important that the column values be in order by key? Will there always be the same number of {key, value} pairs in each of the .db's?

If each .db has the same number of {key, value} pairs, you can build the array in a single large nFile x nKeys vector, which might let you can some creation time at the expense of later access time.