My Plucker files on the card end up under /PALM/Programs/Plucker. I don't keep them in internal memory, but they should be recognized by the program there as well. The should be *.pdb files. I don't use Plucker Desktop, but rather SunriseXP to put the files on my card, so I can't help you if Plucker Desktop's your thing.
Plucker on your Palm should be version 1.8 (or 1.9 if you download a more recent "snapshot" currently in development). Check the version on your palm, and if needed go to
http://www.plkr.org/download and select your operating system near the top. I'm wondering if you're confusing the "Plucker Desktop" on your computer (which is version 1.6.2 for Windows).
I am a big proponent of SunriseXP (started the Wiki for it here on mobileread). I haven't used Plucker Desktop in a long time, but I found that earlier versions of Sunrise were much easier to handle. Check
https://wiki.mobileread.com/wiki/SunriseXP_tutorial for more information on it. Good luck!