Maybe your browser is decompressing the ipk. Some have been known to do that before now. Try a different browser if you can.
The outer shell of an ipk is a gzipped tar file (note: gzipped, not zipped), so try doing this to test your ipk:
tar -tzvf custominput_1.1.0_arm.ipk
If that fails, either the ipk is corrupt or it has been decompressed, in which case try this:
tar -tvf custominput_1.1.0_arm.ipk
If that fails then the ipk is definitely getting corrupted either when you download or when you transfer it to your Zaurus.
I use ar on my linux PC when dealing with Opie ipks, but this is a Sharp ROM ipk.