I believe I have discovered the root cause of this. If you use the command line zip (Inf- Zip) and run zip -rl it will list contents of the zip without extracting.
On the @RUMBLEBOX zip it begins like this:
Archive contains:
flippyfish.pdx/Fish/
flippyfish.pdx/Fish/fish.pdt
...
While the repacked version from @dwineman looks like this
Archive contains:
flippyfish.pdx/
flippyfish.pdx/SystemAssets/
...
The broken zip does not include a directory entry for flippyfish.pdx/ while the working one does. In my reading of the PKZIP specification either is valid (hence why both unzip using normal tools). I believe whatever unzip library implementation included on the playdate device makes an incorrect assumption that there will be a directory entry in the zip prior to a file which is extracted into that directory.
More details over in this thread. Do note that issue is slightly different, as my zip had all the directory entries, but not in the correct order (a sub directory before the root directory).