In case nothing's been found in global cache WAN-accelerator queries the storage in attempt to find datablocks to deduplicate. That is exactly what has happened in your case - the second drive had not been cached due to its not-OS nature
, so the system found duplicate data on your target storage. That's why only 4,5 gigs have been transferred though been never shown in job stats.
However, if you want to have it in your cache, I've come up with a solution which I think can do the trick:
Instead of using two .vmdks you can use a single one and split it into two physical volumes ("OS" and "software") from inside of your OS. In that case the whole VMDK will be considered as an OS drive, therefore everything will be cached including non-OS stuff.
Keeping OS and software drives separate could be important if it was a physical machine (the possibility of drive failure) and/or Windows OS (takes a lot of space --> longer restoration). Since you use virtualized Linux you can easily afford keeping everything in a single VMDK.
Hope this helps.
Please correct me if I'm wrong.