Seriously, I have never programmed a '328 at 3v3. I am not sure what the point of a 3v3 TTL porgramer is, unless you are programming a 3v3 device like an XBee or you do not have a 3v3 regulator on the device for serial communications.
My recommendation is get a 5v0 FTDI breakout and check that out. I will test the 3v3 upload tomorrow on a 8MHz Arduino, but I know that my Seeed Stalker uses 5v0 upload (Board files are 3v3/8MHz) but it operates at 3v3/8MHz. Yes, the 5v0 pin is alive when the FTDI is hooked up.