johnh113 - there isn't any chance you might have accidentally assigned the side volume buttons to a flashcard command at some point, is there? Checking this on a Treo 680 here just now they seem to work fine, but if Pleco was capturing them as command inputs that would stop them from working correctly.
We do need to recalibrate the volume scale on Palm, we jacked up the volume because people were complaining it was too quiet but it seems like that was only a problem on Windows Mobile so apparently the two systems have different ideas about volume scales.
(by the way, any improvements on your earlier problems with sessions taking too long to start / crashing?)
Mator - the Treo 680 uses more aggressive thread scheduling than the 650, I believe, which essentially means that it's more assertive about pulling control away from the program when it has something it needs to do in the background. This is why the audio's getting interrupted (the system puts the audio on hold while it's working to find / select the next card) - unfortunately Palm doesn't really provide developers with any way to control that part of the operating system, so the only way we could stop the audio from skipping would be if we stopped audio playback as soon as you advanced to the next card. (which I imagine would be even more annoying)
The recognizer pause I'm less sure about, but there has to be something else going on in the background there - I assume it doesn't make any difference whether you're using it in the separate Input panel or on the main screen, right? And the handwriting auto-recognize option is turned off in the Input section of Preferences? Pleco really doesn't do anything between individual handwriting strokes (unless it's set to auto-recognize, in which case it runs the recognizer after the specified time elapses) so it's tough to think of what might be causing this on our end - if you're up for it you could always try a hard reset / reinstall, perhaps there's a buggy version of some old Palm OS system library or somesuch floating around in your Treo's memory.
caesartg - not a bug, just part of how Unihan works. The critical thing to remember about Unihan is that it's a character reference and not a dictionary; hence the definition / pronunciation / etc are tied to that exact character rather than a more flexible "entry." That difference is particularly important in cases like 历, characters where a single simplified character maps to more than one traditional - if you look up the Unihan definition for 历 you'll see it's "history; calendar," whereas the Unihan definition for its traditional variant 歷 is "take place, past, history" and for 曆 it's "calendar, era" - to supply a simplified/traditional mix you'd need to consolidate those three entries to two, one with 历[歷] and one with 历[曆] (as in the ABC), and adding that to Unihan would require not only reformatting it but rewriting a lot of the definitions.
The traditional character stroke order diagrams look like that because the company we licensed the stroke order data from didn't have a set of it for traditional characters and created it at our request (and we didn't pay them enough to get them to make them as pretty as the simplified-character ones

) - we've now, however, licensed a different set of stroke order data which we're planning to integrate into future versions of Pleco and that should allow for more similar-looking simplified and traditional characters. (along with some exciting new features like multi-radical search)
Good idea about flashcard audio, we could certainly add a popup list to the audio button to let you set the volume (and maybe also the gender at the same time).
radioman / The Duelist - is either of you using tone coloring by any chance? We just found a bug with that that could cause this exact problem.