Try the Ports line in level at 10. Nothing will be as good as the 301 on a good amp… unless you get the Decca FFSS and cart

I tried this but the sound is still horrible, at a higher volume :-/

Would suggest trying the Ports line in with another source such as CD / DVD … anything with an analogue output and ignore the 301 and the preamp for the moment. Horrible is of course in the ear of the listener so hard to say how bad it is but the port converts analogue to digital and whilst OK for most it’s not acceptable to me.

Do double check and plug back into your main amp, just in case a wire broke.

Many thanks, I checked with a CD player through the Port (with the same cables), and the sound is perfect, as when I stream. 
But when I plug directly the turntable & preamp to my Amplifier without the Port, the sound is perfect too.
 

so that’s definitely looks like an incompatibility, but I can’t understand how it’s possible since it’s just an analog source. 
 

Earthing / switch mode power supply in the pre?

Try the line in level at 1 and see if that helps, unless that’s what it was set at before.

I take it you use the preamp to connect to the Port?

The line in on the Port and the Amp should be exactly the same, when given the same settings. There is no effective difference between each line in. You should, however, double check to ensure that both line ins have the same settings, which frequently can be different.

Amps rarely have adjustable line in sensitivities to the extent the Port has. Port line in settings close to max (10)  is about what the typical amp has as sensitivity.

To summarise, CD player into the Port line in to amp sounds fine.

Turntable pre amp to the amp sounds fine.

Turntable pre amp to Port line in to amp sounds horrible.

Same cables in use.

Mysterious, frankly.

PS: One assumption in the above statements - that in the case of turntable preamp to amp test, the wiring is NOT to the phono jack on the amp, but the same jack as is being used for the CD player or the Port wiring to the amp. If to the phono jack it means that the preamp to amp is sounding fine because the preamp is not giving output voltage to the extent needed for the line level jacks in use for wiring the CD player/Port.

I did some digging into the Atoll and found this about it on their website:

On the back panel there are RCA inputs and outputs, a ground plug for the vinyl turntable, and two ‘DIP’ switches (one per channel). These allow the user to adjust the gain depending on the cartridge (40, 46, 52 dB), as well as the load (100 ohms or 47 kohms) and capacitance (0 or 100 pF). These adjustments ensure that it is compatible with all high and low output cartridges on the market. 

It seems to me that the solution is suggested in the above via ensuring that correct setting are made on the preamp taking into account kit on both side of it. As well as a correct use of the referred ground plug.