After being first reported in April of 2006 (in this forum post), Mahesh Slaria from Kayako told the community how to fix this problem by changing some code (it is not fixed in the current stable build).
For a while now we've had customers with @yahoo.com email addresses complaining about receiving blank emails from our ticket system… after looking at the Kayako forums (we use Kayako support-suite) we found that other Kayako customers were experiencing this as well.
Finally, around 4-5 months later we get a solution:
"Blank email issue is just due to HTML encoding, you can change 'html_encoding' to '7bit' or '8bit' in en-us.php at locale folder of SupportSuite."
Sure enough, we tried it out and it fixed the problem!