First check both your partitions UIDs with Disk Utility (Info on disks), they must be different. Then add this to each of the /Extra/com.apple.Boot.plist files

<key>boot-uuid</key>
<string>UUID of this partition</string>

replace "UUID of this partition" with the real UUID of that particular partition, in the form
XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX

You must do it to both /Extra/com.apple.Boot.plist files, each with its own UID.

From then on, Chameleon will be able to differentiate the 2 partitions /Extra contents