I did not see this issue with the 6.5 beta version. However, with archetype13-based projects, the alpha 6.5.4 version of AEM doesn't seem to update a bundle contained within a package if the bundle is already installed. (I didn't try updating the version of the bundle, since I'm just updating the snapshot version in development.) However, using an archetype23-based project against the alpha 6.5.4 version of AEM seems to work fine.
I determined that with archetype13, the Maven build still generates the correct packages and AEM actually returns a 200 ok message. So, something is going wrong within AEM but I didn't see any related logs being generated and wasn't motivated to debug this since I've moved on to archetype23.
In cases where I still need to work with an archetype13-based project, I just define an alias for a curl command to directly update the bundle (i.e. not part of a package) in AEM and that works just fine.