I use randmax, and yes it will override your settings that you put into Winplan. Have you set your default tax up for Growth Tax or Safe Tax?
If you're setup for Growth Tax for instance and one of your planets has native happiness around say 55%, then it will set tax rate to zero for a bit to recover the happiness.
Also make sure you haven't set a "minimum natives for taxing" or "minimum income for taxing" or something like that in the config file, as these will influence wether the natives get taxed at all.
if you like, post through your randmax ini file for us to look at