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I don't know why it was set to the older default then. I'm 100% sure I did not change this setting and always remember seeing the warning in the compilation log.
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Stupidity is hard to eradicate from software :)
What version of Quartus are you using? It must be fairly new to support this device. Create a new project, select that device, and then look at the setting. It sounds like the default will be the stupid value. Repeat for a Cyclone IV device and you'll see that the default is the sane value.
Cheers,
Dave