Comment 2 for bug 1121950

I can confirm the bug Christophe has reported.

Assume a clean database with multi company setting enabled.
Using Admin account create the following company structure (go to Settings >> Companies):

1. Main company M
     1.1 Company A
             1.1.1 Company A1
             1.1.2 Company A2
     1.2 Company B
             1.2.1 Company B1

Then, create new user login (go to Settings >> Users), UserB as Christophe said and set the Company field to 'Company A' and put the following under Allowed Companies: 'Company A', 'Company A1', 'Company B1'.

Under Access Rights, set the Administration field to either 'Access Rights' or 'Settings'. Which one you choose doesn't matter as the bug manifests itself using both of the options.

Also set any other installed module to at least 'User' so UserB can see the top-most menu.

Log in as UserB and go to Settings >> open UserB by clicking on it and go to Access Rights section.
What you'll see in the Allowed Companies field is: 'Company A' and 'Company A1'. 'Company B1' is not in the list!

The only 'workaround' to see 'Company B1' is to set UserB's company to 'Main company M' using Admin login.