I have run into a problem where jquery does not initialize correctly when loaded after the dom is ready. It seems like this is a problem in jquery.mobile.core.js. Well not really a problem in there, but the fact that jQuery Mobile is depending on the dom not being ready as the script is executing. In a perfect world the script would be included in the header and the dom inits would not fire until the script has finished executing completely. But if jQuery Mobile is included in the dom after the dom is already ready, the dom-inits run prior to the rest of jquery mobile executing causing problems with initializations.
I was able to "fix" it simply by changing the build file to put jquery.mobile.core.js at the end of the concatenation steps. I use the ant build script. Im not familiar with make or I would have contributed a change to the source.
It sounds like a good idea to change the build to put the core at the end, anyone familiar with the way it is built today want to comment on why it is and if moving core to the end of the concatenation is a good idea?