I've never used the lead free solder (other than in plumbing, where I despise it), but as a thought, are you using the same iron tip, and if so how long have you been using it with the leaded solder? Purely speculation on my part, but could it be cross contamination with the non-leaded residue that might still be on the iron tip? (Obviously this isn't the case if you're using a new tip.) If you haven't swapped tips and happen to have a spare, it can't hurt to try switching.
Additionally, what are you soldering to/on? A circuit board? Could there be trapped moisture present that's boiling off as you solder?
I've never seen bubbling like what you describe in leaded solder, and am interested in hearing what the cause ultimately turns out to be.
-Pat