Maybe you have a micro leakage. If the rough vacuum is not okay the turbos don't increase their speed. It's a kind of protective function. Another source of error could be the electronic of the turbo pump. A few years ago I had a similar problem with a turbo pump.The pump only increases up to 50 % of maximum power. Cause of this error was a defective fan on the electronic board of the turbo pump. Changing the fan and turbo works fine again.
Don't misunderstand me. When I write fan I think of the fan on the electronic board - not the turbine wheel inside the turbo. In this case your turbo doesn't start and you have to buy a new one (R.I.P.).
Sounds very much like your turbo controller, although at 3.5% it easily could be the pump. You can tell by taking the pump out and seeing if the vanes freely spin. If they don't then it is the pump; if they do it is most likely the controller.
Also check whether all your necessary o-rings are in place. Creative people sometimes forget to put them back where they belong after opening MS sources.
I have a brand new 5973 MS couple to gc during pump down process it displays that the turbo is on but the speed is at 0.0 % although during the installation we mistakenly interchange d the controller cable with that of the turbo but when realized we interchanged them but still show 0.0% speed. Pls where could be the fault