I know it's not the same thing, but I've had issues with my Wicos where, occasionally, they'll do the same "clicking" that you describe after I've dis-assembled and then re-assembled them. In those situations, the spring around the shaft is also very tight and it's difficult to put the e-clip back on.
Clearly, in my case, there is something inside that's not quite lining up correctly. I've never been able to identify exactly what it is, but I believe it has something to do with how the spring sits and compresses.
Again, I don't think this is exactly what you're describing, because the spring on the Wico doesn't affect the tension of the joystick. The tension is a product of the rubber grommet, but beyond that, what you're describing sounds very familiar to me and my solution is to basically take them apart and re-assemble them until everything sits correctly.