Managed Metadata appearing in wrong columns after Restoring a site to a new Site Collection

I've restored a site with some libraries that have Managed Metadata (MM) columns from one site collection into another site collection inside the same web app so it should all subscribe to the same Managed Metadata
Service Application.
There are two MM columns in one library, one holds a single value which is what type of document it is, the other is a general tag field that allows the user to add multiple MM values to it if they want.
What we've found is that data has randomly disappeared on some MM fields, on others it appears in the wrong column, and in other cases it appears fine.
I used native out of the box GUI backup and restored with the command line,
I've done it twice with the same result, so it’s not a one off corruption during backup. It's the same story in a different doc library based on different term sets as well.
Of all the things to not work properly, MM was probably last on my list to expect, it's knocked my confidence in it a bit, as well as worried me about future upgrades.
If anyone has any ideas over what may be the cause of this, it would be appreciated, I've read lots of blogs, but nothing quite like this has cropped up.
Thanks,
Jon

Most of the ISV offerings will allow you to 'Migrate' content from one SP location to another. I'm pretty sure AvePoint and a few others have tools specifically developed for shifting bits and pieces around SharePoint farms.
It is a limitation but the ISV tools tend to do a good job and maintain nearly full consistency.
There's scripts around that can do much/most of the migration and you could always extend them to do the same things as the ISV migration tools however the cost to do so can quickly get to the same ballpark as buying an already made tool.
Paul is also in the London office, we often work together when projects requiring his brains and my beauty crop up.

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From here:
http://www.c-sharpcorner.com/uploadfile/anavijai/programmatically-set-value-to-the-taxonomy-field-in-sharepoint-2010/
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Managed Metadata appearing in wrong columns after Restoring a site to a new Site Collection

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