Since updating to
[2011-10-23 16:23:29 - Dex Loader] Unable to execute dex: Multiple dex files define Lcom/myapp/R$array;
[2011-10-23 16:23:29 - myProj] Conversion to Dalvik format failed: Unable to execute dex: Multiple dex files define Lcom/myapp/R$array;
My problem was resolved after cleaning up some directories and files left over from the previous versions of the tools. ADT Rev 14 changes where binaries are stored. I deleted the entire bin directory, restarted Eclipse and cleaned the build and forced a rebuild. That seemed to do the trick initially but the problem came back after the next run.
I finally discovered that my bin directory was included in the project build path. I excluded bin from the build path and repeated the steps above. This resolved my problem.