I wouldn't worry too much about the difference between 60 and 90. Adding it earlier will probably cause a very slight darkening. Personally I wouldn't worry about it, but if you are, add it later.
To me this is the only real difference. The longer you boil the more color/melanoidin/carmelization/Maillard reactions you're going to get out of the syrup.
If Im doing a Dark Strong, or darker beer where I want that added stuff I will toss it in the beginning of the boil. If Im doing something where I want it to be light in color, like a Golden Strong for example, I add it in the last 15 minutes or so of the boil. I personally, like Denny havent noticed much yeast stress or anything like that....I should note that I never used light candi syrup, plain sugar works just as well in my experience. So usually for me its sugar going in around 15 minutes, darker syrups going in near the beginning of the boil.