Yes the bot has been updated significantly, and will have many enhancements in the future.
To answer your question, Your alts will show under your main using the !admins command. If you give someone leader or admin rights, you give that rights to all their alts as well. Vhabot sees alts of a admin/leader as the same person as the one you gave rights to.
Is there a reason you don't want their alts being admins?

If you are the admin on the bot, you should be listed as Super-admin and any registered alts.

also...
Did you upgrade to .81 using your old config data from the last merger?
If so, the character ID's have changed and the bot wont recognize you on the new server. The id's will conflict.
We tried to preserve the data from the old rk1/rk2 to the new server but there are too many issues with it.
If this is a fresh bot you made, let me know and I will try and get to the bottom of why you are not listed as an admin. I am running .81 myself and he function is working properly.