Arduino-on-a-breadboard and serial communication help

I have two questions here...
I built the arduino on a breadboard as described on this website (atmega328p-pu, serial connection using a FT232RL USB module on RX/TX pins with 10k pullup, DTR connection through 104 ceramic capacitor to reset pin along with another pullup) and serial communication is messed up. I can still upload sketches using the manual reset AND I can send serial data using the same method, but if the atmega is already powered on for some time (ie. 3-4 seconds or so) I simply cannot communicate with it at all. So my question is: any idea on what I could try/what could be wrong (I always get the out of sync error, maybe it's related)? Or is there a way that I could send data from a linux computer (not more than ~5-10 characters or one integer usually) to the atmega without using the hardware serial connection (I have a COM, LPT, USB and sound ports/headers)? If I can't send strings it's all right but I'd like to be at least able to send GPIO signals using a python script on the computer end.

Also, could I send those signals simultaneously with boblightd on the serial port or I would have to find a way to disable it temporarily on the computer before I could send anything to the atmega ?

Thanks!

Investigate the DTR/Reset part of it for wiring issues - it sounds like DTR isn't resetting the chip like it should.

Use serial to communicate between computer and Arduino. Anything else is a lot more work, even when the hardware is working correctly. Here, the hardware is not working correctly, so you should fix that and use serial.

Does your sketch use the serial port?

DTR connection through 104 ceramic capacitor to reset pin along with another pullup

So you have 2 pullups on Reset? Or, just 1 10K pullup, as in this example?
0.1uF caps on the VCC & Avcc pins are also important.

@DrAzzy Thanks for the tip...that's what I thought at first. I bought new capacitors and wires and I'll try rewiring everything on the reset pin

@ChilliTronix I'm not quite sure to understand the question...I have to use the serial port if I want to upload sketches?

@CrossRoads Thanks for that schematic! I used the one from the arduino on a breadboard page here on arduino.cc but that schematic is somewhat different. I actually have one 10K pullup on the reset, one one the TX and one on the RX pin only. I did not know that a diode was required between RESET and the +5V ? And R1 is 110K ohm ? Also, I need a 0,1uF between VCC/aVCC and +5V ? I'm curious to know why that is required ?

EDIT: Oh I misread... One 10k pullup and not 110k pullup.