SInce many people are reading this and no one has replied, I'll add some more info...
1) I tried re-creating the time lapses with no luck. This is strange to me, because the preview video which was rendered for Adobe Audition had no problems. I do recall updating Premiere since rendering out that, so I suspect that may be part of the problem. I may have to try a computer with an older version of Premiere CS6 to see if that helps, however it will be some time before I'm able to do that.
2) I tried converting the time lapses to After Effects compositions, and it did not help. I get a new error when trying to simply play the newly created composition in After Effects, which while I don't remember the exact error, it was something along the lines of 'the file has a different size than the software is expecting' or something like that. I'm not in front of that computer at the moment to re-create the problem for an exact error. To troubleshoot this problem, I opened several of the JPEG images in the time lapse in Photoshop, and re-saved them as a new file. I got this idea after reading around that sometimes it helps. No luck whatsoever.
I don't really understand why I'm having so much of a problem now. I suppose I may try to render out the time lapses as video files, import them into the sequence, and see if I can get that to render out, however I am concerned about the quality of rendering something through twice just to get it to work, as well as the fact that it seems I have to use an older version of the software simply to get an output.
Is there anyone at Adobe that can look deeper into this to see if it's a bug or not? It's seriously affecting my ability to use the software for it's intended purpose, especially considering I'm using features that are part of Premiere, and I have no extra plugins installed. I spent a great deal of money on the Master Collection as well as the computer capable of running it very well, and while I'm aware there wont be software developers lurking around here all the time, it's a bit of a blow to not have any response so far about this.