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Rocksmith around 30% of the time wont recognise notes played on the A string both open and fretted

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Hi everyone

I play Rocksmith 2014 using a fret king bass which has P/J pickup combo, I have set up the Bass myself really well the truss rod is adjusted correctly  to give around 20 thou Neck releif around the 7th fret, the intonation is spot on, it is very nice well set up bass which i can easily play all the way up the neck with no problems.

However i have now and have had for a long time an issue where Rocksmith wont recognise notes played on the A string in particular, it use to be on both pickups, however i lowered the Jazz bass pickup and i notice the more i lowered it the more responsive it became and the less notes where missed, i now have it riduiculousy low at 4mm above the body and  9mm from the strings at which point it them picked up every note i was paying, however when i want to play using the split coil P bass pick up, it didnt make any difference how much i highered or lowered the pickup it still misses note on the A string i currently have them set at almost parralel with the top of the  body which is way lower than anyone would normally have them set but notes are still missed on the A string to the point where i have now just given up using that pickup when playing rocksmith which is a shame as it is a hand wound pickup with really excellent tone which i would like to have the option to use.

I use  stainless steel 45 to 100 Flat wound strings which the nut has been cut specifically to accommodate.

I have done all the usual thing from the rocksmith end like recalibrating  and i found setting the input gain manually to maximum helped,.

I alway play rocksmith through headphones on a PC with the output from the sound card sent to a stereo amplifier  the headphone are plugged into the amplifier but i also have the option to plug the headphone straight into the PC soundcard but both ways the issue is exactly the same, I dont have any issues with latency.

I just wondered if anyone had ever had the same issue and what you might have done to resolve it  ?

my only thought might be that might need to maybe change from flats to roundwounds and see if i still have the same issue

Thanks in advance for your thoughts

The string may not be sitting perfectly at the nut or the bridge causing some extra harmonics that are confusing Rocksmith. You could try taking the string off and putting it back on again, making sure it isn't twisted. Also set witness points. Press the string down above the nut and below the bridge saddle so the string forms an angle over its anchor points and not an arc.

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