sapsaj wrote:
Transparency Flattener Presets is set to low, and won't switch off low.
It only seems that way. In the same way that PDF presets don't affect the layout, Transparency Flattener presets are not used until output and have no effect on screen display in ID. You choose the correct preset in either the export or print dialog.
That said, as Eugene points out, keeping the transparency live is usually a better option.