Just a short checklist of things to try... many of which you may have thought of.
1) check audio settings in windows making sure speaker and recording settings have correct defaults.
2)I'm not familiar with the 6i6 but if it's ASIO, check the asio settings and in particular; some ASIO related hardware have software mixers that may need settings adjusted.
3)If the 6i6 is thru usb, firewire, or a thunderbolt device, you might try changing the ports. This would likely also force a reinstall of the driver if it's plug and play. If this solves your issue then make sure to test that port with another device; a mouse for instance.
4)make sure that you're disconnected from the internet then, turn off your antivirus program. They have been known to interfere with some after-market hardware and can use up resources required by the recording software. It will take priority over pretty much everything for the sake of protecting your computer.
These are just some of the basics. Beyond this, you may consider contacting Presonus CS.
This may not solve your problem but it may help, even if in other areas. I recommend upgrading your computer's power supply when possible. If you're not hardware savvy, most people today know someone that is and upgrading can ensure that proper power levels are sent to the ports at all times which also can solve latency issues when it concerns audio recording or midi input. Truth is, when you buy a computer today, it's power supply is usually just large enough to operate any factory hardware. Add a PCIe card and start filling the ports and that creates power-flow problems. I found out the hard way that this can affect computers set up for gaming or recording the most. After all both usually require additional hardware and high computer processing.
