The original problem was caused by an issue in the way the Activation Status was saved for Layers in 3.2. The Activation status was being saved in two different ways and these where getting out of step with each other.
What I think you are seeing is due to the pieces being saved incorrectly under earlier version of 3.2 and are now that the bug has been fixed, have ended up activated when they should be inactivated or vice versa.
What I need to know is:
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Does this just happen with pieces from saved games or pre-defined setups that where created in earlier versions of 3.2, or does it also happen with freshly pulled pieces?
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Does the Tools → Refresh Counters command fix the problem?
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Does resaving the game and then reloading it fix the problem?
I am away for the next 4 days so will not be able to do anything much till then. My hope is that the Refresh Counters will fix the problem (Fingers crossed!).
If not, I will need an example module and save file.
Brent.