Hi Everyone,
Referring to my earlier talks with Swat_OP R8R, I left IC (inner core) as suggested and made my way to Dervon for blasting some Ancients to improve my rep with DK (Dom'Kavash). It seems something is out of place as after shooting down ~20 Ancient drones my rep with DK has not improved at all.
Following is a quite a rant, I appreciate anyone who has the interest and patience to read the whole story 
I'll try and give summarized details of my CF journey in the following for someone wiser than me to be able o point out what could be wrong:
1. I play CF 2.0 SP campaign with "ENB Standard" shader option, install file downloaded from Swat Portal, all the latest updates installed. Since starting the campaign I have not changed any general gameplay options and played with 'Average' difficulty level all the way.
2. During the campaign I have not visited any of the new CF systems until they have been revealed to me in the SP campaign (e.g. new systems conneccted to X-3043).
3. Here's my journey in nutshell after first arriving to the GMG hypergate in Omega 3 system (mission 31-32?) : I declined to go to IC (and start the mission)the first time I arrived to Omega 3 hypergate as I wanted to explore Altair sector more prior to IC missions. So I went to Sol -> Styx (got Nomad action I was unable to avoid, this perhaps had negative effect to my DK rep) -> Mandar -> did pretty extensive Altair/Coalition systems exploration (did not shoot any DK during this time) -> returned to Sirius -> Utopia -> Dervon for 2nd meeting with Ancients (shot down a few drones but again couldn't avoid Nomad action in Utopia..) -> finally back to Omega 3 hypergate -> through IC systems in order of the mission waypoints laid out (shoot down some Dom'N, Dom'R, Warriors and Savages) -> started missions 33 & 34 with the DK -> got stuck with mission 34 'Device' coz of the rep with DK -> tried to kill some of the other 'Aliens' to improve DK rep -> Got feedback from Swat Portal to shoot Ancients to improve DK rep -> Left IC via Phanchdar hypergate -> through Altair to Yakutsk and via dimensional anomaly to 'Unknown" (had to shoot some Nomads again - DK rep suffered a bit) and Omicron Gamma -> to X-3043 via Omicron Alpha.
At this point (after reaching X-3043) I realized that oddly factions that I have maxed out negative rep with (CSF, Outcasts, GC etc.) appeared 'neutral' in my ship scanner/radar and did not become hostile to me unless I attacked them. I then went to Dervon to shoot down the Ancients and the drones also show up 'neutral' in my scanner even my rep with Ancients is almost maxed out negative (-9). As mentioned before, after merking about 20 Ancient drones my rep with DK is unchanged. 
As you probably understand, I'm reluctant to reload back to original 'Dervon mission' as there is pretty extensive gameplay between that mission and my current savegame. 
So Dear seasoned vets and CF gurus & anyone who might be able to share tips. help or ideas for solutions, your feedback is most welcome. 
May the Force be with ya'll!
[edit:system name X-3043 corrected]