1. It seems to assume all albums are by a single artist. I have a number of compilation albums that consist of multiple artists, and I'm not sure how to sort these in the CSV file?

Right now, you will have to sort them with everything else, by Artist. The album won't stick together, because the interface itself is hardcoded to be grouped by Artist, then grouped by Album, etc. It was a decision I had to make based upon the limitations of the Palm platform and the .pdb format. Generally, most of your albums will not be compilation albums anyway, but I will look into this later as a possible feature (grouping by album).

2. It's skipping about half of my songs. Could this be because about that many are missing one or more of genre, year, track number, and (in the case of singles) source.

Yes. You can see in the java code that if I don't have exactly 9 comma separated values per line, it skips that line. This is because creating the .pdb file from a .csv file is not going to be the way to create your database, it will be an option in Jemplode, and I did not want to waste time coding for all the limitations of a .csv file. Mike Schrag is working on releasing a new version of Jemplode with an updated internal node structure very soon, and as soon as that happens, I will modify that code to work directly from Jemplode. Then you will get all of your tracks, regardless of how you have tagged them.

As an aside, I have all my tracks tagged with [Single] for album if there is none, and in extreme cases [Unknown].

3. The PDB file isn't uploading fully to my Palm. This could be a problem with my setup, but I've not had difficulty before, so is it possible that a partially corrupt PDB file is being generated?

I saw that you fixed this, but I had to make sure that nothing else was interfering with my Serial port before uploading could occur successfully. My .pdb file is over 400k, so it takes a long time, but my IR port on my laptop was causing it to blow out around 100k. If anyone has problems Synching, it can probably be googled for and solved easily that way.