Question: Were they meant to be the same entity?

If they weren't, does this imply that Borg have distinct "hives"?

Out-of-Universe, the actresses playing the roles were all mixed up, but sounds like Paramount originally wanted the same actress implying it was the same Queen (or merely that all Queens are 'clones'?):

From <http://www.imdb.com/name/nm0860749/> (Susanna Thompson):

> 
> **Trivia**: Got the role of the "Borg Queen" on Star Trek: Voyager only
> because Alice Krige (who played the role in the movie Star Trek: First
> Contact) refused to reprise her role.
> 
> 
> For the final episode, Susanna Thompson was not available (because of shooting *Once and Again*) so Alice Krige played the Borg Queen in the final episode.
> 
> 
>

Answer: 
I don't think this was really fully addressed in the movies or TV series, but the [memory alpha](http://en.memory-alpha.org/wiki/Borg_Queen) page seems to indicate that they are not the same physical bodies, but they might be the same personalities - the Collective simply upgraded a drone to be a new queen when the old one was killed - much like how hive insects behave.

> 
> The death of a Borg Queen did not seem to affect the Collective or its hive mind. When a Borg drone died, its memories would still be within the hive mind.
> 
> 
> ...
> 
> 
> The Borg Queen that was present in 2377 was assimilated when she was a child, together with her parents.
> 
> 
> 

As Katey points out in her comment, Krige played the Queen in both the movie and the Voyager finale. However, a different actress was used for the other appearances throughout the Voyager series.

This could also mean that they were two different Queens, and that there may be two separate Collectives (one in the Delta quadrant, and one nearer to the Federation).

Unfortunately, it does raise a problem in that the Borg Queen seen in 2378 (Voyager - Endgame) was the same physical body that had gone back in time from 2373 and been killed in 2063 (First Contact).
She said in First Contact that, the Borg before her it was just havoc and chaos, where the Borg where (running around like a chicken with its head cut off) when she was assimilated she took over and brought unity and formality to the collective.