I dont know if this will work for you , but I have heard of people
using
rope as a filler (regular anchor type rope, but much MUCH thinner)

It stays flexible enough for expansion and contraction and should
stain to the same oak color.

Again I read this somewhere and dont have any practical experience
on this yet. (I do have a similar problem on some of my oak floors in
my house)

I will try to correct that soon though...