Before I start, I should mention that while I wasn't looking the game updated to 1.1.1, so if there are residual issues that might be at fault.
I tried the fixed dll that you provided and it seems to have fixed the problem, but for the sake of completeness I thought it wise to provide you with another simulation log so that you can verify that the changes you made are having the desired effect.
I had the game create a fresh output log, and then had the game run a verbose simulation on the 17 part craft, and then created a new vessel of the same configuration as the one in the picture I posted earlier and ran a simulation on that. Here is the output log for those tests: https://www.dropbox.com/s/f076g5wni12wv9j/output_log%202.txt?dl=0
If you need me to test anything else out for you, just let me know.