JB Jr sounds 'out of phase' on it's own if that even makes sense

Hello recently installed a Jb Jr into my strat, never use one before, but I am used to hss strats. It just sounds really off, like super quacky (almost wah like sound) and is quieter than my single coils despite having a 14k resistance (I checked it). The only thing I have heard sound like it is out of phase pickups, but it sounds like this on it's own? I installed it will a push/pull for coil split and it sounds fine, like a low output single coil when coil split. Not sure if it's just I dont like how the pickup sounds if there is something else going on.

For reference with fender pickups, red and white together, green to 5-way, black to ground. Any ideas?
 
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Well, the JB Jr shouldn't sound like that, so something is not quite right. Have you tried wiring it directly to the output jack to see if you get the same quacky sound? You wired it correctly when mixing it with modern Fender pickups.
 
Sometimes pickups leave the factory being wired incorrectly. Try swapping red and green, so red to the switch and green with white together. That should help in that case.
If it helps, but the pickup is out of phase with the fender single coils, then instead of red and green swap black and white (white to the ground and black with red).
 
Try the wire swapping suggested by htrd. If that doesn't help, or if it makes it sound worse, then welcome to the club of recognizing just what a JB sounds like.
 
This isn't very common at all, but has happened before.

Wouldn't QC help to handle this? Thinking of how pickup winding happens in general, and how precision and attention to detail are required if one wants to be able to obtain consistent results, I'm trying to imagine a situation where the winder manages to mess up during the process and end up with one coil wired the wrong way. As in, dropped the bobbin on the floor after finishing laying the wire? Even then, it's easy to figure it out. Very intriguing...
 
The QC in this case is not easy. You can test the coils for their DCR and their inductance. You can even check the strength of the magnet and the orientation of the magnet, but doesn‘t say anything about the orientation of the coil.
 
Wouldn't QC help to handle this? Thinking of how pickup winding happens in general, and how precision and attention to detail are required if one wants to be able to obtain consistent results, I'm trying to imagine a situation where the winder manages to mess up during the process and end up with one coil wired the wrong way. As in, dropped the bobbin on the floor after finishing laying the wire? Even then, it's easy to figure it out. Very intriguing...

Well, you can notify the factory if that is indeed the case (and it was bought from an authorized dealer). My guess is that they would ask you to ship it to them and they would get out a replacement quickly. But that is if you can confirm what is going on.
 
Even the best QC can't be 100% accurate. I've met miswired pickups, misprinted labels (Pagasus instead of Pegasus for example) and I even remember seeing on this forum a Dimebucker with a print on the wrong coil. Sometimes this happens, not a big deal.
Pickup winding and assembly is not a rocket science and doesn't require any exceptional precision, it is rather routine and monotonous work, so a worker can accidentally take the wrong lead wire when soldering it to the pigtails.
Swap the leads and call it a day. If that is the case, of course (:

The QC in this case is not easy. You can test the coils for their DCR and their inductance. You can even check the strength of the magnet and the orientation of the magnet, but doesn‘t say anything about the orientation of the coil.
Inductance test will show it, but I assume that QC tests only for resistance.
 
My JB Jr. bridge also sound like it's out of phase clean, but distorted it's actually quite nice, it too has lower output than I expected (APS-1 in the neck is louder).
I wonder if that's just how they sound or something wrong with my JB Jr. as well.
 
My JB Jr. bridge also sound like it's out of phase clean, but distorted it's actually quite nice, it too has lower output than I expected (APS-1 in the neck is louder).
I wonder if that's just how they sound or something wrong with my JB Jr. as well.

You have to check to see if it is wired correctly. First, check to see if both coils are working (by tapping on them with a screwdriver when plugged in). The JB Jr is a loud pickup, and will easily overpower single coils, so either something is wrong with the pickup or wrong with the wiring.
 
My JB Jr. bridge also sound like it's out of phase clean, but distorted it's actually quite nice, it too has lower output than I expected (APS-1 in the neck is louder).
I wonder if that's just how they sound or something wrong with my JB Jr. as well.

Definitely check the wiring in your guitar.
 
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