While testing the built-in automatic unwrapping function for generating lightmap UVs I recognized some seams on mostly roundish (cylinders, spheres) objects.
Should I unwrap them manually for proper lightmapping or are there some proven values for the advanced unwrapping parameters to better deal with these shapes?
Best solution is to place two sets of uvs on your meshes. Your texture can read off of one uv and your lightmap can read off the other.
Here is a max tutorial by the way…http://forum.unity3d.com/threads/23203-3dsmax-lightmap-small-tutorial
You might be able to write a custom editor script and tweak the default automatic UV2 generation parameters to see if this helps with your problem. If it does, then you could save the modified model as a “.asset” file and then use that in your scene instead.
This is just an idea, but it helped for me.
I’m not sure about this, but I have the exact problems too. The UV unwrap pre-3.5 was fine (I still have builds from it where the seams are correctly placed / not that visible).
Did you experience this problem before updating or is it me imagining (again) something… 
[double posting… forum doesn’t let me edit my posts]
Using a higher Pack-Margin helped a bit. Nothing beats doing your own UV2 though. Looking further, I don’t think it’s a 3.5 problem anymore so disregard my previous comment.