I've had a number of FCs, and I think that one important issue is making sure that your bridge stays vertical over time, not exerting too much stress on one aspect of the adjuster. I'm not always a perfect citizen about monitoring this bit of basic maintenance.
Yeah I'm still leaning towards that ultimately being the issue.... something creating uneven pressure on the wheel. I've leveled the contact area that abuts the wheel but I'm thinking the downward force from the strings to the adjuster is uneven just enough to cause issues but not be overtly visually apparent. It's just odd because I'd expect that to cause the pickup to cut in and out as things are manipulated but it's either 100% working or not working, there is really no in between.
My bass has a couple small rib cracks that need to be addressed and I plan on having the Bass Cellar guys double check the leveling of the bridge when it's there. If I haven't gotten it figured out by then I think that will help. I'll also try the replacement FC when it arrives but I'm hesitant to believe the pickup itself is at fault.