known issues about (long) tracks alignment?

Hi everybody.

I just got this problem:

- I import an audio track on which I want to play (from the file selector.) e.g., a drum track.
- I arm a new track for recording, connect my guitar to my soundboard, press rec+play and start recording. No delay, no latency, no strange things in my ears.
- I export my tracks (from the Master output)

I close Qtractor.
When I load my bounce to Audacity, I notice that what I just recorded is not correctly aligned (guitar starts too early)

So I open Qtractor again and now if play all, the tracks are actually non aligned. So I align them and do the bounce again.
Same problem.

I noticed that the track I imported is a mp3 file at 44.1 K frequency, while JAck and Qtractor were set to 96 K. So i thought: "this is the problem".
I set my system (Jack and Qtractor) to 44.1K, started a new session, so everything was now set to 44.1
I recorded again the guitar, I made the bounce and.. same problem. Guitar and drum are not aligned anymore.
But, closing and opening Qtractor again, the guitar seems to start properly now, and after a while, what I recorded (or, how Qtractor was now playing) went out of timing again.

What can I try? Are there some known issues of this kind?
Could it depend on the sound board?
I'm quite sure when I was still using my old (now dead) sound board, this wasn't happening.

Thank you all
Manu