I'm running 10.6.8. They are all HD versions (I generally record everything on my TiVo in HD), so I don't know if it only affects HD programs or not. If it matters, my cable provider is FiOS.
The programs in question are hour-long shows on cable networks; some examples of shows that I've been having problems with are "Burn Notice" (USA), "Eureka", and "Alphas" (both SyFy).
What EXACTLY happens is that I download the show using TiVo Transfer, and that works fine (that program is unchanged as we all know). I'll bring it into Toast, and then I'll start editing it to remove commercials. I'll be dragging the pointer to find a commercial, and at some point, I'll get the "rainbow pinwheel" for a few seconds, then the dialog box with the aforementioned error pops up. At that point I can SOMETIMES press "Ok" and get back to the main Toast window; if that doesn't work then Toast is hung and I have to kill it. These points appear at different spots in different files, but they're always the same spot in the same file.
You can avoid it if you don't have the editor window show the bad frame; for example, if you know where the bad spot is, you can type in the clip point you want in the boxes below the video window and create a clip point just past (or before it). Figuring that out, however, can be a challenge.
Once you create the clip points, the video transcodes fine. If you just hit "play" in the editor window, you can play past the bad spots fine.
If you really are interested, I could provide you a sample video and my MAK key. But the affected ones are something like 6GB, so it's not exactly something I can email you