Taking a guess here while I wait on an answer to the comment, generally when a package runs fine in BIDS but doesn’t work from the commandline, I find it’s related to 64/32 bit incompatibility.
Are you using Excel, Access or anything else that under the sheets uses the JET driver? That only works in 32 bit mode.
On a 64 bit OS, by default when you create a new ODBC connection, you’ll be creating it in the 64 bit namespace which the 32bit version won’t be able to access?
Are you using Informix or UDB/DB2 drivers? I only ever found 32 versions of those.
Running a package from the command line
dtexec is the command line mechanism for running an SSIS package. It comes in 2 flavors for 64 bit OS, both are named dtexec and generally the 32 bit is referenced in the Windows Path environment variable
On a 64 bit OS, the default path to the 64 bit would be "c:\Program Files\Microsoft SQL Server\100\DTS\Binn\DTExec.exe"
Still on 64 bit OS, the path to the 32 version would be "c:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\DTExec.exe"
To run a package named FooBar.dtsx that lives in C:\Src\MyProject\MyProject, invocation would be
"c:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\DTExec.exe" /file C:\Src\MyProject\MyProject\FooBar.dtsx
If that package lives on SQL Server (DEVSQL01) in the folder MyProject, this would be the call to run the same package.
"c:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\DTExec.exe" /SQL \MyProject\FooBar /SERVER DEVSQL01
Edit
To apply a configuration, you need to specify the /CONF option
"c:\Program Files (x86)\Microsoft SQL Server\100\DTS\Binn\DTExec.exe" /file C:\Src\MyProject\MyProject\FooBar.dtsx /CONF C:\FooBar.dtsConfig
Looking at your comments, the only difference between our usage is you have wrapped everything in double quotes. Try it without the preceding and trailing quote.