I do experience that too sometimes and I've found it only happens on large venues with when I'm using predominantly low end like reggae for example. Never heard it with any gig where I'm using a more full range sound.I think it's mostly from not having good/consistent monitors. I generally have a solid ear and I don't have any injuries that I'm aware of at this moment. I've wondered a lot of it's some kind of phasing issue with monitors vs PA or something to that effect. I'm gonna start researching in-ears. I think that's the next step for me.
This very thing happened to me this past weekend on the second of the two large festival gigs i played. I used a different bass for each gig and a different rig but on the last gig I was using a mesa boogie 2x10 and a walkabout head. Tuned up at soundecheck and noticed the slightly flat sound and in fact it was more evident when I asked for more volume in my monitor as the gig progressed. I too have wondered in the past if it is a phasing issue as between the cab and the monitor adn the side fills. I don't use effects at all so that is not a component and it is the same situation whether or not i'm using ear plugs or not. I'd be interested in finding why that is.
As a slightly aside point. A few years ago I had some custom moulded ear plugs made and found that when I use them on gigs where I slap, the pitch again sounds slightly flat. I called the company who made them and they said this is something that has been mentioned to them a few times but they currently have no idea what the reason is. It doesn't happen when playing any other finger style and most of my gigs don't involve slapping so I continue.