I own a couple devices like that (Tascam DR-07 and Sanyo ICR-XPS01M) and well, I'm just using Audacity for the cuts and then the files are ready for the video editor.
Can't help because I can't verify the issue but it sounds like you need to get with SonicStage support and supply them the files that don't work,.
Bob
Hey there,
I just got a Zoom H4N, and I use SonicStage. I'm importing wav files that are over an hour long, I've had a zoom before and (it got stolen) and everything worked fine. Now with this new zoom, it's importing them as 43 second files that don't play anything. They play, they work fine... just not in the program! I can convert to MP3 and get them to work but that defeats the purpose. Help!
They are... whatever it is, the 44.1 - 16 bit files... standard, SonicStage says it can support them.
Help help!

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic