The command line to run a miniscan is usually like so (for reference):
ldiscn32 /mini /o=C:\MyMiniOutput.txt
The "/O=..." switch creates an output file.
The "/mini" switch tells the inventory scanner to create a mini-scan.
Whilst you CAN do this, it's usually easier to capture things on the Core side (but either works).
If a (later) FULL inventory scan has got the serial number, you may want to cross-check the version of LDISCN32 in your WIM image versus the one in your LDLOGON directory (could be "just" a case of an old scanner version, for instance).
You could TRY sending the data (if you can get to it) as a custom data string (separately) via the following (I'm not sure this hack'll work, but it's something to look at potentially) -- How to send Custom Data with a Miniscan .
Hope that'll help?