The only solution I have found is to name my main file the same name as the application within the project. My application runs fine when I do this.
[Note that this has been edited to match @Idan Adar's recommendation above. It's not the PROJECT that must match the mainFile, but the APPLICATION name]
The following works fine:
Project name: MyProject
main file: MyProject.html
application-descriptor.xml: <mainFile>MyProject.html</mainFile>
worklight.plist: <wlMainFile>MyProject.html</wlMainFile> (this is a generated file)
It appears that Worklight launches the iOS application properly the first time using the file specified in wlMainFile. Then when it has to resume or restart, it's looking for the application name rather than the value specified in wlMainFile.