Thanks for posting.
With the new FileMaker 12 layout design we do expect to see some increase in file size post-conversion dependant on layout heavy solutions.
Here is an excerpt from the FileMaker Pro 12 Help topic Converting files from FileMaker Pro 11 and earlier:
"Converted files may be larger than the original files. Part of the conversion process increases the file size of databases. Though the size increase is typically not significant, the increase varies by file. Make sure you have adequate storage space before converting files."
That said, if it's possible, I'd like to get a copy of your 3.4 MB clone to do some research here.
I've sent a private message to you with instructions on how to send me that file. To check the message, click on the Inbox link located in the upper right corner of this forum.
I recieved the clone of your database; thanksfor sending it in!
I'll forward the file along with my research to our Development and Testing department.