What we have seen so far is multiple reports from people saying they were using various tools for only window layout, etc - but that they still received a warning email about software broadcasting tools. It appears that none of the existing tools (Innerspace/ISBoxer, AHK/HKN or Keyclone) are OK to use - even if you do not use the key broadcasting features. We've even had a few report of people being flagged that don't even have more than 1 active account - but they still have the software running for various non-multiboxing functionality.

It appears that Blizzard is scanning for the presence of the software itself and flagging accounts based on that.