Arduino ATmega1284p bootloader

php-freak:
Yes, thats right, I have caps on both sides (0,1µF). On my FTDI there os GND, CTS, VCC TXD RXD and DTR. I thought DTR is the auto reset pin so I connected DTR to Pin 9 with a 0,1µF cap.

This is my FTDI programmer: http://www.ebay.de/itm/230820610037?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1497.l2649#ht_500wt_1414

Again, thanks a lot for your help!

First you can use either RTS or DTR as the arduino IDE/AVRDUDE pulses both signals to generate the auto-reset pulse. The oldest auto-resetting arduino boards used RTS, all the newer ones use DTR, but for legacy backwards compatibility the IDE pulses both RTS and DTR signals.
Second, what do you mean by "I have caps on both sides (0,1µF)" ? if the DTR (or RTS) signal has to pass through two series .1ufd caps to get to the reset pin on the avr chip then that is an effective capacitance of .05ufd and may be too small a value to allow the pulse to generate the reset. If that is the case remove one of the two series connected .1ufd caps from the circuit.

Lefty