Trigger the bug then look in the *messages* buffer.  Search for one of
the groups that did not update.  Did gnus correctly classify the
group?  What type is this group (i.e. primary, secondary, foreign)?
What type did gnus report?

>> So, here's the next test.  In your group buffer, type
>
>> M-: (gnus-activate-group "GROUP")<RET> {where GROUP is the group name
>>                         as shown in the group buffer.  Obviously pick
>>                         a group that is not updating.}
>
> M-: (gnus-activate-group "INBOX")<RET>
>
>> What does this function return in the minibuffer?  If it is nil, your
>> group isn't activating.
>
> It returns `nil'.

OK, so the actual problem is somewhere inside of
gnus-activate-group (We'll come back to this with the next message).

Here's an interesting test.

Try this
M-x load-library gnus
M-x load-library gnus-start.el
M-x gnus

Has the error gone away?