I’d have to play around with the plugins you’ve listed to see what wp-minify is doing to break them. From what i recall though (experience from past issues) it was usually related to this things methods to shrink. It would strip out an important white space under a certain condtion in javascript code or something. Eeeks. I remember way back there was an issue with jQuery and this thing because when we looked we noticed jQuery changed something that made the code more ambigious and hence would break a plugin like wp-minify (it wasnt minifies fault, but jQuery for not using explicit brackets) but i believe a few of us here simply added brackets in our versions and were done with it.
I will have a look at those plugins when i have time next week and see how they behave. It will always give me time to refresh my memory on this plugin. Last time i worked on it WordPress was at v2.8…but amazingly the plugin has never had an issue since.