Command-Line Build with eclipsec and Virtual Folders/Files appears to ignore virtual files

I'm trying to build a few projects from the command-line using eclipsec.  Here is the call:

C:\ti\ccsv5\eclipse\eclipsec -noSplash -data "../temp_boot" -application org.eclipse.cdt.managedbuilder.core.headlessbuild -importAll "../Bootloader_I2C_EEPROM" -cleanBuild "Bootloader_I2C_EEPROM/Debug" -build "Bootloader_I2C_EEPROM/Debug" > BootBuild.txt >&2

It fails with the libc.a compatible library issue when I try the boot project I have because it doesn't find any source files (they are virtual).  The larger projects have a mix, since a few are thrown in the project folder and brought in automatically by Eclipse and everything else is a virtual folder/file.  My command-line build scripts for those fail with linker errors because it doesn't include the virtual files in the build.

Is there a fix for this? 

(I don't have program mode compilation turned on, as another poster found fixes his/her problem). 

Thanks

Operating Environment
CCS v.5.1

Windows 7

C6457

Scripting Language: Dos Batch file