amzipkin
The smoothing spline code is based on:
Hutchinson, M. F., & de Hoog, F. R. (1985). Smoothing noisy data with spline functions. Numerische Mathematik, 47(1), 99-106.
Hutchinson, M. F. (1986). Algorithm 642: A fast procedure for calculating minimum cross-validation cubic smoothing splines. ACM Transactions on Mathematical Software (TOMS), 12(2), 150-153.
The smoothing parameter is determined automatically when "AutoSmooth" is selected. See those references for the details on that. If a specific level of smoothing is selected you are effectively selecting the "p" parameter in the above references. Note that if you do not have enough selections in your reference material group Spline_AutoSmooth will default to other options: >=6 selections will use auto, 4-5 will use medium smoothing, 3 will be step linear, 2 will be linear fit, 1 will be mean.
I can have a look at one of your sessions to see if I can spot anything causing your problem. Send an example (any raw data + logs or io4 file, as well as any necessary reference material files) to the iolite support email if you want me to.
All the best