Mike - the reporting tool isn't perfect.
I've just run it. I'm using RANT (not Linux), but ... the results are probably similar.
I have two RA licenses - one for 8 seats, one for 1.
The tool reports 2 license keys, but says I have 16 in use - "Buy more!"
- the number in use is correct - 9 remote servers, 1 Exchange server (which includes the RA in the license) and 6 workstations (for which you don't legally need a license)
So, the tool is reporting the number of keys, but does not "read" the key for the number of seats, and doesn't exclude workstations.
In your case, the 1 license key is correct. My concern would be that it only reports 1 in use - looks like an install problem on that second server to me.
Cheers