The problem isn't in build 32. The problem is that your script & methodology for configuring dnsmasq is wrong and never worked except accidently. (Also that the script is not easily understandable, and nobody is going to spend the time to debug somebody else's incomprehensible script. But that's another matter.)
The way Tomato handles dnsmasq is what it is. Customised scripts have to work with it as it is, not as they wish it was.
To repeat what TB said, what you're doing the custom config file is wrong. Period. The fact that you never observed it to fail was a fluke. It was never right. It just accidently worked sometimes.
If you really want to make an automatic, user friendly script, what's wrong with http://tomatousb.org/forum/t-262221/ ? Although I should really move it into the tutorial section.