PrE 7 Installation Corrupts Accuracy of Synching when Using Visionary Software

Question

Hi !
HERE'S ONE THAT WILL DEFINITELY BE A CHALLENGE FOR SOMEONE WHO THINKS THEY KNOW WHAT'S "UNDER THE HOOD"!!!!
We do video strictly for use by attorneys in legal cases.  In addition to standard editing, we need to provide them with files that literally synchronize the text from the transcript with the video (the video is first encoded to MPEG1).       There are a number of programs that do this, and the one we use is "Visionary" (Visionary Legal Technologies).
As other such programs do, Visionary uses voice recognition to align the audio from the MPEG1 file with the transcript.
For very basic standard editing of depositions, only because of the ease of use (as well as some of the features that are conducive), we previously used Pinnacle (Avid's basic version, such as Elements is Adobe's basic version of the Pro).  There was no problem, and everything functioned normally, other than a few minor glitches with Pinnacle (one being occasional audio/video synch issues when burning).  For that and a couple of other reasons, I felt like Elements would be a more solid foundation for editing, and would solve the synch and other issues.
HOWEVER......, something occurs when installing Elements, that has to do with it modifying the standard Windows (XP) codecs.  Visionary absolutely REQUIRES ALL of the EXACT STANDARD Windows codecs  (MediaPlayer, Media Encoder, etc.).  There cannot be one single change, update, or anything whatsoever done to alter ANY of these.  Period!!
Honestly, I didn't connect the dots at first, but for some reason, Visionary became inaccurate in its voice recognition.  It started out fine as usual, but as each 1 to 2 hour long MPEG1 video file progressed forward (from the beginning toward the end), the audio gradually became more and more out of synch with the text in the transcript.
After a ton of time, it was determined that the installation of Elements 7 was definitely the culprit.  It did something, such as replacing some of the standard Windows codecs, that was positively, without question, the very cause of this problem!  Uninstalling Elements did not even fix this, but,  interestingly (and luckily) when rolling back the WindowsXP registry (restoring to a date prior to the Adobe install), Visionary went back to working just fine!!
This may imply that the codecs or whatever other files may not have actully been completely overwritten (theoretically, a restore couldn't bring back erased files!), but alternatively, somehow did cause the entire OS to default to the files that Adobe replaced (or at least added), and in the process, rendered the original files/codecs as obsolete.
So, the question becomes; how can we have both Adobe Pre-Elements and Visionary on the same computer without having even the SLIGHTEST effect on ANY of the original Windows files/codecs that MUST remain completely unchanged from their original form in order for Visionary to work? 
In other words, it's fully understandable that Adobe may say that whatever they're doing to the system shouldn't affect any of this, and what they're putting in is "better" for all applications than what is furnished by Windows, but unfortunately, that is not the case!
Whoever can resolve this quickly so Visionary can work as it's designed and still have Elements on the same machine without it touching anything whatsoever that Visioniary needs, I'll buy dinner!!!!
THANKS BIG TIME!!!!        
Les

Answer 1

Thanks Hunt!  Good explanation of the appending of the names, and I appreciate that!
The anwer to your question is yes, after uninstalling and rolling back the registry, it did put Visionary back to working properly.  That's why this is confusing.  Maybe I'm slightly off track with the assumption of what it did, but we know for a fact that the install sure did do "something"!
You seem to have a finger on that pulse, so, do you have any other ideas about what could have changed to cause this conflict that messes up Visionary, beside my speculation?
I was thinking, that, if there were only some way to install PrE7 on a separate drive, without it even touching anything at all anywhere in the OS folders, that would undoubtedly reslove it, because it wouldn't exist or alter anything in the machine at all.  Obviously from the limited mid-level knowledge I possess, I've never imagined that such would be possible with any Windows based program, but in theory, something on that order would at least do the trick.  (As with most programs,I know, for various reasons, it definitely cannot be done that way for Visionary's software).
Ridiculous as it may sound, is there any possible wayto accomplish SOMETHING in that concept range?  Of course, I appreciate your explanation, but if can lead to some sort of a work-around, that would be, by far, the best!
Thanks again!
Les