Charlieplexing code doesn't reset the state of unused pin and if the port value is HIGH + mode INPUT, it means the pull-up is enabled.
Solution is reset all pins to LOW before code starts changing directions. And the last step would be setting correct pin to HIGH.
If you want to do it in single loop, you might observe really short pulses (it might or might ...
I'd start by cutting it down to just the setup() and loop() functions (without the timer call) and establish whether it connects, and if not, why not.
Then add back the timer call and a very short version of checkSensors(), and try again.
Continue adding back sections of code until it fails.