Further I put bubble level on the tonearm's bearing housing, it showed unlevel (the turntable itself is perfecty even) which might cause the above issue.
Well, when an Armboard is not level, you will ruin your cartridge pretty fast.There are so many different forces for it, it can't survive. Your cantilever will be bent sooner or later. Well, of course it is possible that you have also different VTF based on that, but the other problems are much more serious. Did you also hear a shifting in soundstage in the last 3 tracks?
Is it a DIY board?