on the commandline I include a Base Schema, Schema A, and Schema B. There's no import statement used in there, I just make sure the proper namespaces are defined and I can use objects from Schemas A and B in the Base Schema. But I also have Schema C, which I'm not including on the commandline, and it's being imported within Schema B.

I run the following command:
echo "abcd,efgh,ijklm,ABCD" | ./daffodil-core/target/start parse -s daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_base_08.dfdl.xsd --root base2 -s daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_A_08.dfdl.xsd -s daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_B_08.dfdl.xsd

and this is the output:
2013-02-27 06:58:51:326 edu.illinois.ncsa.daffodil.compiler.Compiler Error [Compilation (ProcessorFactory) produced 1 errors/warnings.]
2013-02-27 06:58:51:332 edu.illinois.ncsa.daffodil.compiler.Compiler Error [Schema Definition Error: Unable to import namespace http://c08.com from XML catalog(s) jar:file:/home/jchab/NGF/dfdl/daffodil-lib/target/scala-2.9.2/daffodil-lib_2.9.2-0.7.0-SNAPSHOT.jar!/daffodil-built-in-catalog.xml, ./xcatalog or schema location edu/illinois/ncsa/daffodil/section06/namespaces/multi_C_08.dfdl.xsd. Searched these locations:
Schema context: import. Location in file:/home/jchab/NGF/dfdl/daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_B_08.dfdl.xsd]

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! An unexpected exception occurred. This is a bug! !!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Please help us fix this by opening a bug report at:

https://opensource.ncsa.illinois.edu/jira/browse/DFDL

Please include the following exception, the command you
ran, and any input, schema, or tdml files used that led
to this bug.

edu.illinois.ncsa.daffodil.exceptions.Abort: Usage error.
edu.illinois.ncsa.daffodil.exceptions.Assert$.abort(Assert.scala:85)
edu.illinois.ncsa.daffodil.exceptions.Assert$.usageErrorUnless(Assert.scala:69)
edu.illinois.ncsa.daffodil.exceptions.Assert$.usage(Assert.scala:60)
edu.illinois.ncsa.daffodil.compiler.ProcessorFactory.onPath(Compiler.scala:85)
at edu.illinois.ncsa.daffodil.exceptions.Assert$.abort(Assert.scala:85)
at edu.illinois.ncsa.daffodil.exceptions.Assert$.usageErrorUnless(Assert.scala:69)
at edu.illinois.ncsa.daffodil.exceptions.Assert$.usage(Assert.scala:60)
at edu.illinois.ncsa.daffodil.compiler.ProcessorFactory.onPath(Compiler.scala:85)
at edu.illinois.ncsa.daffodil.Main$.createProcessorFromSchemas(Main.scala:129)
at edu.illinois.ncsa.daffodil.Main$.run(Main.scala:309)
at edu.illinois.ncsa.daffodil.Main$.main(Main.scala:501)
at edu.illinois.ncsa.daffodil.Main.main(Main.scala)

I've tried using a full path with my import, updating the classpath, etc. but still get the same error. These are the files I use:

A daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_A_08.dfdl.xsd
A daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_B_08.dfdl.xsd
A daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_C_08.dfdl.xsd
A daffodil-test/src/test/resources/edu/illinois/ncsa/daffodil/section06/namespaces/multi_base_08.dfdl.xsd