Some turnout decoders do not work when the red and brown wires have been swapped.
Red goes to B or centre rail, brown goes to 0 or outer rail.

Maybe these five decoders require a particular polarity and maybe polarity is reversed with the MS2 vs CS3.

First of all – thank you for your suggestions.

Some updates after a lot of testing yesterday:
• I tested one of the non-operating turnouts – connected the CS3 to a single track – it operated as expected
• I split may layout in 2; and was able to operate the previous non-operation turnouts most of the times:
• The 1st half of the layout operated finally after a lot of testing, but when retested after a while, still problem with one turnout. This turnout I tested separately connecting the CS3 to a single track – it operates as expected; but not when put back in the layout
• The 2nd half of the layout operated as expected when testing the turnouts. Put on a BR 81, I experienced problems switching the turnout when the train was nearby; the started also to flicker after a while

I checked all wiring, both under the tracks, and the distribution – found that some of the flat sleeve connectors did not fit tight to the track – adjusted them, but still the same problems.

I also monitored the track current with the CS3 – one of the halves had almost 0,5A power consumption in idle state. I understand that this is way too high, so I connected the CS3 to a single track, now I had 0,3A; which I understand is at least 10x to high.

Removed the track connection plug from the CS3, still 0,3A power consumption. Something with my CS3 – HW or SW?

My track layout is around 20m, power distributed before and after all turnouts, together to other parts of the layout. Is it recommended to add a booster (60175 + 60041)?

Looks like not enough power to the layout. Booster may be needed. Try taking everythinrg that uses power off the layout and see if all the turnouts are working.

Hi Arnstein
The track does not draw any current in itself (only switch decoders and lanterns do).
Seems to me, 0,3 A for a limited number of switch decoders (and no loco, no train?) is very high unless, of course if you use M track and bulbs in lanterns. By comparison, my layout, with 50 points with lanterns, 26 sound MFX trains and more than 30 lighted vehicles needs 2.7 A and 3.3 A when all is moving.

Not sure it is your case, but built-in switch decoders are just great for "Teppichbahning" but disastrous for a permanent layout.
To power a couple Decoder + Switch motor trough many track contacts is bad and lead to non-frank commuting of switches

Yes spade connectors are very convenient but you quickly understand that plugging such a connector in one orientation and then the other means one orientation gives flimsy contacts so you may have the "tighten" the connector for better contact and always plug them with the same orientation - the open lips of the female connector are always facing down in my case.

Just my 2 cents
Cheers
Jean

I have verified the polarity and everything is OK

I reinstalled my CS3, and added the turnouts again - same result...

What is strange is that I have no problems operation the turnouts with the MS - whish has a smaller power supply than the CS3. I have 1,5mm2 cables for the distribution, and 0,75mm2 to the tracks

I have power feed on each side of the turnouts, and are using 1,5mm2 cable for the distribution, and 0,75mm2 cable to the tracks

Are the switch decoders the new mfx ones or older?

They are the new version with the DIP-switches facing down. I have set the addresses on each turnout with the DIP-switches - understand that this also could be done automatically with mfx?