Thanks guys.
We're having a little difficulty reproducing this here -- to clarify, we're sure it's happening to you, but just need to check a few things to see if it's the conduit that's misbehaving or the BigOven installation itself.
Can you try the following on your PC?
1) First, find out which folder BigOven is using as a "Palm staging" folder on your PC. This is found in the Windows registry (Start/Run regedit.exe... then navigate to HKEY_CURRENT_USERS\Software\SDMVentures\BigOven and look at the "PalmDir" key). Generally, this location is your "Shared Documents\My BigOven Recipes\Data\Palm" directory.
2) Now, open up a windows Explorer Window to that Palm staging folder you found, and run BigOven. Try selecting a few recipes and click "Publish to Mobile". Be sure to click down the Palm icon button. Watch the "Palm\Recipes" folder as the "recipes" folder fills up with a bunch of .BGO files for those recipes. Verify whether or not it's behaving as you expect.
3) Now, publish some more recipes to that folder, unchecking the "clear all recipes first" box.
If you could report back to us to let us know whether that directory is filling up for you as you expect (without HotSync), that'd be helpful. Thanks!