The manual safety body plunger and spring are on the left, and the revised ambi lever plunger and spring are on the right.
You can see how the body plunger spring is much heavier than the ambi lever spring. It can't easily be compressed between your fingers, while the ambi lever spring can be.
New ambi plunger springs are painted light blue.
Body plunger springs are unpainted.
The original ambi lever plunger looked similar to the body plunger, having a machined shoulder below the head,
but the end was flat (not fully rounded like the body plunger). Mixing up the early plungers could result in a grinding noise during decocking/lowering the safety levers, as the flat top of the ambi plunger wouldn't move as smoothly inside/against the slide as the round top of the correct body plunger.
The later, revised ambi lever plungers have a straight profile and a wide head. The levers were machined differently to fit the heads of the different plunger shapes. (I can't remember the last time I looked at a 645 ambi lever/plunger, but I was once told the .45's may have gotten the got the straight ambi lever plunger first, before the 9/.40 guns.)
Mixing up the springs can result in a couple of problems, too.
First, putting the heavy body plunger spring under the ambi lever is difficult, as the spring doesn't compress as easily as the proper, lighter ambi lever spring. If an armorer can't easily compress the spring in order to slide the ambi lever in place ... that's a hint the wrong spring is under it.
Second, the lighter ambi lever spring isn't strong enough to properly tension the manual safety/decocker body plunger when recoil forces are acting on it. The usual symptom of having switched springs, and having the ambi lever spring under the body plunger, is that when the slide cycles the gun can "decock" itself, and levers remain in the On-Safe condition as the slide returns forward. The ambi lever spring doesn't have enough strength to properly power the body plunger to prevent the manual safety/decocker body from rotating (lowering the levers, as it were), as the slide slams to the rear.
Not being able to inspect your 6906, I can't know what noise you're hearing, and what it might mean, if anything. (A clean gun can make some louder noises than a gummed up, cruddy gun, though.)
As an armorer, I've never experienced either of those plunger springs "wearing out", even on early 3rd gen guns we had in-service since '89/'90, but then my exposure was on a small sampling of maybe 500 guns (and later on a similar number of TSW's that replaced the early guns).
Doesn't mean a spring couldn't have been damaged at some point, or defective. They're just springs.
Got a gunsmith in your area who is familiar with S&W TDA pistols, who could inspect it?