3.3V & 16MHz - not a good combination.
Am sure that impacts sketch downloads too - mismatch in serial rates.
Programming via the SPI pins overcomes that.
Go spend 30 cents
http://www.dipmicro.com/store/index.php?act=viewProd&productCode=XC6-80000
or less!
and get the right crystal. Dipmicro is by Niagara Falls, very inexpensive shipping.