It actually is changing the password for the user specified with the --user flag. I've verified this by checking the password stored in the Qube database; it does change for the user specified, not the user who ran qblogin.
I'll put in a bug report; it makes sense that it should show who it's changing the password for, not who's running it.
burk-17-mbpro:datawh jburk$ qblogin --user foobar
Current User: jburk
Current Domain: .
Windows password:
Retype password:
INFO: updated password.
jburk-17-mbpro:datawh jburk$ mysql -u root -e "select user,passwd from qube.passwd\G"
*************************** 1. row ***************************
user: foobar
passwd: 11adfbdc1cc196eb82952d005e192cd9ff3ae7a9a5a492251558bce3403f0a2f
jburk-17-mbpro:datawh jburk$ qblogin --user foobar
Current User: jburk
Current Domain: .
Windows password:
Retype password:
INFO: updated password.
jburk-17-mbpro:datawh jburk$ mysql -u root -e "select user,passwd from qube.passwd\G"
*************************** 1. row ***************************
user: foobar
passwd: 123ff105e8c5282d40688cf2aa6347aa3a1c1736a0925dd8f310e96cacb82560