I am having a similar issue, except I am using an FTDI Basic (https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_2117341_-1) set for 5v.
It uploaded the blink sketch just fine but anytime I am trying to upload anything larger than 2kb it gives me this error:
avrdude: stk500_paged_write(): (a) protocol error, expect=0x14, resp=0x64
avrdude: stk500_cmd(): programmer is out of sync
Bootloader is functional (Might 1284p) and I followed maniacs schematic write up to the letter: Arduino on ATmega1284P | maniacbug
Any ideas why I can change and upload the blink sketch as much as I want but as soon as I try to upload a larger file I get the error?
Edit: I am getting RX TX led activity for about 2 seconds than nothing. On smaller sketches this seems to be enough time to get it uploaded before it goes out of sync? I am so lost...