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I'm having this same issue, only I can't set the VCCIO to 2.5 - Quartus sees that I'm using an EPCS configuration device and forces the VCCIO back to 3.3, at which point I get the same thing. I'm using all of the available I/O pins on an EP3C40Q240, so I'm hoping there is a way to override this using an environment variable, and simply handle the issue logically (make sure access to the EPCS and the RAM are mutually exclusive) Is there any way to demote this to a warning?
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Try followings:
1) At "Configuration" tab of "Device and pin options" set checkbox "used configuration device" and select EPCS which you use; In the listbox below (Configuration device I/O voltage) select 2.5V
If it's not help then
2) Go to "Voltage" tab and set "Default I/O standard" to 2.5V. It must help.
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