That is natural, each acoustic space has its own character and will interact with any sound produced there. So there is no point on using the same eq or gain settings in two different places, you have always to match your tone to each ambient you get. But you should do this in your amp, not on the Bass. Ideally we should know how our instrument really sounds like (as I work on studios, it was simple to figure out mine , since the sound at engineer's sweetspot is - supposedly - fairly flat). You can try a good phone to avoid room acoustics in a flat sound system (or whatever this means) to get used to how your Bass sounds independently from amps or rooms.
This is not so easy since each phone also sounds differently, though. But this is the only way to not get too biased by room natural tone. Once you know exactly how it sounds bare naked you 'll be able to make any adjustment on amp just to compensate any room or equipment's idiosyncrasy. Remember, your tone comes from your bass and fingers, but what you will hear depends upon how your amp sounds and how they will interact with room acoustics. So, don't change your tone on bass or pedals just because it sounds odd or different on any room, use your amp to compensate this and make it sounds back like it should.
