@Mark > Have you updated the firmware on your CDJ's since you've bought them?
If not, please check HERE and update if necessary.
Please also note that just because both the CDJ's say 126, does not mean they are both exactly the same. If 1 track on the CDJ-350 is 128 BPM at 0% pitch, and another track on the other CDJ-350 is 132 BPM at 0% pitch, you cannot simply increase the pitch % on the 128 BPM track until it says 130 BPM, and decrease the pitch % on the other track until it says 130 BPM to be at the same tempo.
On the CDJ-350's the BPM's have certain ranges of which they display a specific tempo. If the CDJ displays 130 BPM, that means it will display 130 BPM from the point of 129.50 BPM up until 130.45 BPM. So there is some room for error and could be where you are noticing the difference. Using the above scenario, the track that increased to say 130 BPM would only be at 129.50 BPM if you moved the tempo fader until it first read 130 BPM. Meanwhile, for that track you decreased to read 130 BPM, the track would only be at 130.45 BPM if you only moved the tempo fader until it first read 130 BPM. So to be honest, you would almost be 1 entire beat off per minute and that is noticeable.
Please note, the BPM reader on any type of CD player should only be used as a reference to ballpark what tempo you are playing at. For fine adjusting, a DJ should always result to using their ears and match the beats and tempos together. :)
If the case is what I mentioned above, then you should try using your ears to mix more before trusting the BPM readout. ;)
As far as using CD's and regular files on a USB device, sometimes the BPM count isn't always 100% accurate and can sometimes provide a slightly different result than the actual BPM. This is why using your ears is much better.
If you want to receive accurate BPM readouts on your CDJ-350's, you should use Rekordbox as it should have been provided with your CDJ-350's. It's a free music management software that analyzes your tracks and allows you to export them to a USB device and be used on supported CDJ's. Rekordbox will analyze your tracks and provide you with an accurate BPM readout every time. But if not, you can quickly adjust the beat grid within the Rekordbox software to correct it.
By using Rekordbox analyzed files, you should always have accurate BPM readouts on your CDJ's, but please note it will not change the way the CDJ-350's display the BPM. You will still need to adjust the tempo and beat match the tracks by using your ears, as a DJ should always do. ;)
I hope this helps. :)