For all the years using Showgard mounts I have never found a method for "flattening" wavy mounts. I usually feel the package before I buy them. I do know most dealers will replace them if you send them back.
However, since you say your mounts are old I guess you are out-of-luck. I will use the non-wavy portion of the mount for narrow items. If narrow they seem to flatten out on the page.
The back of the mount is also a little more transparent when held up to light than a flat showguard mount.
I have noticed that also. It may be a production flaw.
One reason I do not use Scott or Prinz mounts is that they all seem that way and also feel flimsy.