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I have had the same issue
The fix for me was to run maintenance using disk utility - I had lots of erros that needed fixing (disk warrior still not 5.2 compatible yet) from the clone, repair permissions, and using leopard cache cleaner, to clean all caches (deep cleaning). I suspect something in my boot cache was screwy in addition to the fixes done by disk utility. Before doing that I reset the pram and fixed permissions (which didn't solve the problem). You might want to start with pram reset as that is where the machine stores boot info. Also, are you sure your battery is holding up ok? At least for me, all is now well. Other weird symptoms I had included various cloned boot drives not having proper names when I booted using option key.
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