I pushed a fix for this 8 days ago. The bug, as far as I can tell, was in failing to set the “don’t try to be helpful and guess the data source of this goal” flag. That is supposed to happen when you change the source back to manual from IFTTT or Zapier.
Have you set a goal to “Manual” and then had it overridden and switched back to IFTTT in the last 8 days? I just went through the steps locally to reproduce the bug, and it does seem to be fixed to me.
Prediction: if you go and set the data source to “manual” now, it will work as advertised and remember the setting next time data is added by IFTTT.