Power issue on connecting controller to FTDI programmer
Perhaps you're inadvertently powering the Programmer via the Tx pin on your Controller. It wouldn't be the first time a chip has been powered through an input pin. This can produce some funny results. 







simulate this circuit &ndash; Schematic created using CircuitLab

As a good rule, never apply signals to a chip that is not powered. 

Many chip inputs have over-voltage protection diodes that connect directly to the chip's supply pins. 

If the chip is not powered, and a signal is applied to an input, then the internal input diodes conduct, and the chip becomes somewhat powered by this input signal. 

This is a bugger to find, if you're not expecting it (especially while prototyping).