If the device is behaving oddly, but the mode pins are correct in iMPACT, could the device still be getting into the wrong mode?
Yes, even if the mode pins are correct in iMPACT, the device could have mis-sampled the mode pins.
The mode pins are sampled on the rising edge of INIT. If the mode pins are being driving by another device on the board and their inputs change at the same time as INIT, problems can arise.
The status register which contains the mode pins picks up the mode pins independent of the sampling done by the configuration controller. Therefore, the pins can read back properly in iMPACT although they transition during the rising edge of INIT and cause problems.