[Help] Capacitance meter project

I've made a capacitance meter based on this tutorial , but with a few modifications, and i'm getting some errors. I've tested both on a protoboard and on simulators, and both worked perfectly, but when i moved to an universal board where i soldered everything the values read were all wrong.
With anything up to 500nF it is showing less than 3nF, and with a 10uF cap i'm getting 16nF. I think that maybe there is a problem on the soldering which is causing that, since on the simulation i'm getting the right value, and i don't think that the variance on resistors and whatnot would made such a big difference on the readings.

Link with the code (Some comments are written in portuguese)

The schematic is the same as the one on the tutorial, i just used the Atmega328 standalone and used a LCD screen.

Here are some pictures of the circuit: LINK

Maybe the problem is on the Aref pin, here it says to put the the pin to 5V, which was what i did, but i've also read that i need to use a 100nF capacitor there for decoupling, do you think that it could be it?
I just tested again on the protoboard using the arduino board (i don't have another crystal to test the atmega standalone), and it is working normally.

I'd say your universal board, whatever that is, has a problem.

Your board layout looks like an issue. Your long wires will have both capacitance and inductance. You have lots of floating inputs and outputs on the Atmega 328.