When you go into the Control Manager calibration screen, there are a group of "Raw Data" values. What are they showing with with the stick at full left, at center, and at full right? That shows you the data coming from the hardware, it's the only display that actually shows the data without going through some modification first and will tell you whether the hardware is working correctly or not.
Also, the center values should be too far off 128. It's not real critical, I think I'm getting just over 100 on one of mine, but if it's way off that can create problems.
The other settings, the ones like "Sensitivity", "Deadzone", etc. If you're using a map, then the settings are made at the axis they apply to in the map itself. If you're just running in Direct Mode, the same setting are available in the CM Calibration screen. There's a tab up at the top labeled "Axis Settings". Select that and you'll have eight sets of settings, one for each possible axis.
The first thing to check is the "Centered" box. For axes that return to center, usually just the X, Y, and R axes, the box should be checked. For other axes that don't center (throttles, toe brakes, sliders, etc.) should generally not be checked. There are times when you might want to do it, but those situations are pretty rare.
It's important to have that right, because Deadzone and Gain are only active when the "Centered" box is checked, and the Sensitivity is scaled off the two ends. If it's unchecked, then no Deadzone or Gain, and the sensitivity only affects one end or the other.
Once that's done and if the values aren't wildly off, a broken wire or something like that sending it down near Zero or up around Max, then the calibration should correct it. You'll always need a little Deadzone on a Centered axis. I think the default is "4", but you need to make it large enough so that whenever you release the stick or pedals and it goes back to center, the scaled value is 127-128 without the need to actually move it there. If you just let the stick pull your hand back to center, the scaled value should go to the 127-128 value.
You can't see the calibrated value in the calibration screen, though. What you see there is just what's coming from the stick. The X/Y grid and the axis bars see the scaled values, but they're under-resolved, they're showing you 1 pixel for a change that should be about 3 times that, so you can't really see what's there.
The trick is to Download the map. Then open up the Calibration Screen. It will list one or more "Control Manager Devices", pick the one that has the axis you want to check. Look at the Raw Data display again. The CM does the scaling, that becomes the Raw Data for the Map, and so the Raw Data will show you what's really going to Windows. Mins should be 0, Centers should be 127-128, and Max should be 255. If it's a non-centering axis, then Min should be 0 and Maxx 255, no center. Either way, run that test with the Sensitivity at 100% or it will show up as a high min or low max for a non-centered axis. For a centered axis it will show both those.
If you do the Deadzone test there, get the stick back to center as you would when you're flying it, then it should always come back to 127-128. If it doesn't, you need to increase the deadzone enough that it does (Centered axes only). If it takes more than you think it should, you probably need to replace the gimbal mechanism, it's usually just worn to much for a set of reasonable settings. You'd need to contact CH for that. It seems to me they used to sell them on their "Parts" page but I don't think they're there anymore.