Robert_Charlton - 8:13 pm on Jul 22, 2013 (gmt 0)
Were the match type settings the same in both tools?
Your question brings to mind what happened when a large change to the keyword tool was made in 2010. Google started basing its data on different Google properties.
Possibly the same thing is happening again, but the differences were much smaller then than what you're reporting here. I'm guessing it's either a glitch or a different match type.
See these discussions from 2010 for reference...
Google Keyword tool - Showing very inaccurate data
Search Suggestions Overhaul - Just Before the Google Instant Launch
Quoting a Google employee, back in 2010...
...This is because the previous version of the Keyword Tool provides search statistics based on Google.com search traffic AND traffic from search partners, while the updated version of the Keyword Tool provides search statistics based on Google.com traffic only. We've updated these statistics based on user feedback, and hope you find them helpful for keyword selection.