The packager is including the externals of some of my externals.
For example, if you look at the last few zips for Grid, you'll see that inside the AceGUI-3.0-SharedMediaWidgets folder (which is specified as an external in Grid's .pkgmeta) there is a second copy of AceGUI-3.0 (which is specified as an external in AceGUI-3.0-SharedMediaWidgets' .pkgmeta).
Is this a bug, or an intended change? I've never noticed it occuring before, though I confess that Grid is the only addon I use the packager for, and I don't know that I've ever looked that closely at the zips it creates.
Actually, it looks like the packager is having trouble with "tag: latest" too.
The latest tag of AceGUI-3.0-SharedMediaWidgets (using this example again because it's the one actually causing problems) isv3.4.1, released 2010-07-25, but the packager is giving Grid a much older version. I'm not sure which version exactly, since I'm not going to checkout each verson from SVN and compare, but by the files included, it's r26 or older. It could be the last tag before that, v3.3.2.
I manually embedded libs from my up-to-date standalone copies for the r1370 release I posted over on WoWI (unfortunately I couldn't use it here too since WowAce doesn't allow file uploads) and found that several of the other libraries the packager had included were similarly outdated, though none of them were causing any functional issues due to age.