Actually, yes, I've now seen this.
After upgrading 10.1 SP2 HF1 to 10.1 SP2 HF5, the Published charset for the project Language Variant was reset from UTF-8 to SERVER. SERVER - in this case - equated to Unicode so when publishes started, things broke in a major way.
What does this have to do with duplicating placeholders? :)
At the same time, any new placeholders I created on templates would get duplicated in the instance of the template exactly as you described.
I've done nothing but set the Published charset back to UTF-8 which has fixed my publication problems but also when I create placeholders now, I get no duplication. I had to delete and recreate the few placeholders I had created (and had duplicates) but when I recreated them, they no longer created duplicates.
Hope this helps.
Cheers,
Gavin