Ah, Classic applications follow a different set of minimizing rules than Mac OS X applications. Apple in Mac OS 9 used the far right control for "windowshading" windows in Mac OS 9, whereas in Mac OS X used the yellow control to minimize to the dock. "Windowshading" makes windows a single horizontal bar with the title.
You won't be able to minimize either Mac OS 9 or Mac OS X windows the same way as the other operating system with the default installed operating system. One of the haxies certainly emulates having Mac OS 9 "windowshading" on Mac OS X, but minimizing Mac OS 9 windows the same way as X is not possible as far as I know. My recommendation is to upgrade to all Mac OS X native applications as soon as possible, as my FAQ here explains:
http://www.macmaps.com/macosxnative.html
Partly as you can see this is because then all applications will behave more the same way as each other and you won't be surprised by the lack of minimizing to the dock that Classic applications have.
Disclaimer: Reference to links I make to my Macmaps.com website are a for your information only type reference. I do not get any profit from this page, and it is open to the public.