There are situations where current flows backwards through the coil, as son as forward current has dropoed to zero. It happens because the capacitor wants to discharge through the closed switch to ground. This is likely to occur when you have lengthy Off times.
As a test, try substituting a diode where you have the switch which is close to ground. (The diode should point upward.) This changes your converter to asynchronous operation. It should make your life easier even though it may not be as efficient as synchronous operation.