Thanks Alex. I think what I was doing wrong was that my "Modules only" Flex project had the "Framework linkage" set to RSL. This seemed to cause some of the Modules to unload (according to the debug trace output) when several Modules were loaded simultaneously.
My Modules are loaded by a Flex app that loads the framework via RSLs, so the Modules are guaranteed to have all the framework classes available. The Modules don't need to load any RSLs themselves. On my Modules project, I changed the Framework linkage back to "Merged into code", however I manually modified the Link Type of the framework.swc to be "External". If I use charting, I would have to make the same change to the datavisualization.swc. This is confusing because the Framework linkage says "Merged" even though this is not true. It seems that a 3rd option should be added to Framework linkage called "External". I probably create a lot more Module projects than full-blown Application projects. On a Modules project, if I could set the Framework linkage to "External" and have it change all the Link Types like it does for RSLs, that would be a nice convenience and eliminate confusion.

