Embed paths in compc vs Flex Builder 3

We have a large project that we need to create an automatic
build for. We have many different packages which have classes using
the Embed metatag to include resources from an assets folder. We
don't have any errors when building our Flex Library project with
FlexBuilder3 but when we build using compc it fails with an 'unable
to resolve [file] for transcoding'. If we copy our assets folder
into the folder where our class resides then the error goes away.
It seems the the FlexBuilder resolves the path from the root of the
project while compc resolves it from the class location. Is there
an explanation for this inconsistency?

If the path starts with a slash character, Flex first
searches the directory of the MXML file for the asset, and then it
searches the source path. You specify the source path to the Flex
compiler by using the source-path compiler option. For example, you
set the source-path option as the following code shows:
-source-path=a1,a2,a3
Flex first searches for the file in a1/assets, then in
a2/assets, and then in a3/assets. If the image is not found, Flex
searches for the image in the SWC files associated with the
application.
If the MXML file is in the a2 directory, as in
a2/testEmbed.mxml, Flex first searches the a2 directory and then
the directories specified by the source-path option.

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