Hi Rob,
This is not a bug, but a limitation of the main updater application that applies to all platforms. On Mac OS X, the PixInsight Core application bundle shouldn't be renamed; it should always be "PixInsight.app", mainly because the bundle is digitally signed, and renaming it and/or changing any of its file attributes may invalidate the signature. If you want to have several bundles (for example, several versions), better keep them on separate folders.