LinuxCNC on Debian Stretch

Did you use this exact command line?
./configure --with-realtime=uspace

Thank you very much

I had a wheezy rtai kernel linuxcnc 2.7 installation and i had base thread jitter 15us.
My hdd died and i have installed to the same system stretch rt-preempt kernel and now i have 140us jitter.
The system is an atom board asrock Q1900M pro 3.
My question is if there is rtai kernel for stretch ?

No there is not (that I'm aware of.)
Why do you think you need Stretch over Wheezy?
There was an experimental RTAI kernel for testing in Jessie, but it had some issues and you will need to compile Linuxcnc yourself if you want up to date versions of Linuxcnc, because it isn't currently supported on buildbot. But there are old outdated (pre J/A Master) builds for it there, that you could at least use for testing latency.

I also have the value of Jitter increased from 7,000 to 40,000 when moving from Debian Wheezy i386 to Stretch amd64

Memory should have no effect, unless it's some memory bank issue that 8GB allows parallel access to different banks and 2GB doesn't? Many motherboards have two different colored memory slots, you need to fill them in correct order to get full memory speed.

I have been using stretch for a year now. I too needed to increase jitter values quite a lot. But this is my daily desktop machine, so it's a trade off between linuxcnc and other work, and I feel that it's still worth it.