actually with guitars I don't notice it, with a xylo (glock) I do. glock is tuned to 440Hz per my tuner, so am I
OK, a little Physics lesson here (I studied this stuff in college). String instruments have inherently in tune overtones - they are harmonics of the fundamental, meaning they occur at integer multiples of the fundamental frequency. This is because most of the restoring force comes from the tension in the string the stiffness of the string is constant with respect to frequency. When a string gets big enough in diameter, the stiffness of the string starts to become an issue, so....we use a small string (for low stiffness) and then wrap winds around that small string to add mass, so the thing can resonate a low frequencies.
OK so what?
Xylophones, glockenspiels, marimbas, vibes (all those things where you hit a bar to make sound) are inherently different - the stiffness of the bar is what provides the restoring force. That stiffness is NOT independent of frequency - it's a dispersive medium, which means that the sound travels though it at different rates for different frequencies. That means the overtones are not harmonics - they are not multiples of the fundamental. If you look at the bars on those instruments, some of them have undercuts - that helps get the lowest overtones a bit closer to in tune with the fundamental, but it's not a complete fix.
So, I said before that what you were saying did not make sense to me - bass guitar is an instrument that is inherently hard to play "out of tune". Now, knowing the context in which you're hearing "you're out of tune", things makes perfect sense. Here's the truth:
YOU are not out of tune. YOUR BASS is not out of tune - it's fine. When playing with a glock/xylo/etc, however,
that instrument is out of tune with itself in terms of harmonics, and when heard with your persistent harmonics which are in tune, they clash. It's not your problem, it's an ensemble problem, and there is no fix that will make the bass work better, other than to use flats, so your harmonics die quicker, lessening the time in which you can hear the clash/dissonance. To fix it as an ensemble problem, you might move the parts to different octaves to where you hear that dissonance less. As you're the bass player, and you likely want to keep the low end solid, that probably means moving the other instrument up.