Interesting!! Do you have the tree command installed - any chance you can produce a filtered tree for a given package from the root of your webserver, so that we might have the ability to reproduce this type of issue? It is certainly concerning to me that it was not finding the Archive!
Maybe something like this for one of your packages?
tree -P '*ourPackage*' --prune
We may not be able to reproduce, but it'd be great to ensure that something is not going awry! One issue that we have seen systems have before using this pattern is directory or other filesystem permissions causing an issue on the fileserver for different folders.
My favorite way to test file permissions:
namei -l /full/path/from/root/of/the/os/to/the/file.txt
Or reproducing using curl to access the URL that Connect was trying to read (in the Archive).
I suspect this is pretty low priority for you now, since you have things working, but maybe this will be useful in the future (for you or others). Please let us know if you run into any more issues!! Apologies for the trouble here!