LTC 1060 switched capacitor filter in mode 3: why this output forms:
Take a look at the datasheet for guidance.  The output is only specified to sink 3mA, and you're limiting at about 3V above the negative rail, into a 1\$\mathrm{k}\Omega\$ resistor.  In other words, you're limiting at the point where the output is asked to sink 3mA.
Try resizing resistors as necessary so that the output resistors are no less than 5\$\mathrm{k}\Omega\$ (the data sheet implies that 5\$\mathrm{k}\Omega\$ is the lowest &quot;good&quot; value to use -- I'd consider 10\$\mathrm{k}\Omega\$ or more).