Just downloaded and installed v1.6.02.
Most of the variables seem to be saving properly now. On my machine here is a slight UI delay before you can input the preference variable - this is likely intended and is completely reasonable. However, it does seem that certain preferences that are enabled/disabled with "yes" or "no" are still not working. For example, when setting the "display suggested artists" or the "Auto save" preference you can type "no". The popup will say "Preference changed: oops, please enter yes or no" and the setting does not change. Luckily I want both of these enabled anyway. :-)
One thing of note: If you choose to have the playlist saved to a folder make sure the folder is already created in iTunes. If the folder does not exist Pedro creates a blank copy of the playlist in the root of the library.