Hard to say what's happening with your file. I just did a test with an obj population using a power fractal as density shader, saved it, reopened it and populated it again. Works.
So I'm not sure, why it doesn't work for you.
Did I get that right? You said that you have to relink the objects each time you open a newly saved version of your file. How does the "Object maker" slot in your pop look? Is it empty? If you click on the + of your pop, do you see your obj file, and it's disconnected from the object maker input? If so, it's definitely not normal.
Of course objects have to be repopulated again when you just opened your file, but TG does this automatically, when you hit render, unless you have created a population cache before. Have you tried that? With a cache the population should be already there, when you open the scene.
However, it's probably impossible to see what doesn't work without inspecting your file. Maybe you can upload it here?
