Buck boost converter output voltage dropping over time
You are trying to run a charge pump from another switching device.  In general, it is best not to run this type of device from the output of this type of converter, when the capacities and switching frequencies are close.  The TPS61222 relies on voltage feedback to regulate, and your LM2663 is providing a load which is changing at its switching frequency.

I would try to run the charge pump generating your negative voltage directly off VBatt as a first choice.  If this is completely unacceptable, you could add a cap to the feedback point of the boost converter, although this will slow down the converter's response to changes in input voltage and output load, possibly causing overshoot and undershoot.