I doubt that Adobe has any nefarious plans to attack the files from any program.
What happens if you Open those files in SoundBooth, Audition, or even the free audio-editor, Audacity? Do they Open fine there?
Are the WAV files PCM/WAV?
While PrPro will work natively with 48KHz 16-bit PCM/WAV files, after Conforming to 32-bit floating point, it will usually work with many other common Sample-Rates, like the CD-standard, 44.1KHz. It just might take a moment longer to Conform to 32-bit floating point.
When you attempt to Import those "problem files," what happens? Do you get error messages? Do you wait for the Conforming to take place? This ARTICLE talks a bit more about the Conforming process.
Thanks for the response. Due to the intermittent nature of this problem I wanted to test more thorougly and can confirm that the files are PCM at 44.1Khz. The error message is, "The file format is not supported", and IIRC the files opened fine in Flash (which will be explained later). Audacity successfully opens the files.
I have resolved the issue and discovered exactly where the 'fault' lies.
Adobe determines the file type by it's filename - rather than using methods in Cocoa library or by looking at the RIFF header. My files are titled, "yyyy.mm.ddName" (Reason/Record does not automatically add the extension in this case), however some files were titled "yyyy-mm-ddName.aif". The former (with periods) would result in the filename extension being truncated from the file's name, but the file 'Kind' is still identified as an "Aif C Audio".
On OSX, any file with an unknown extension should also have it's file type checked using the Cocoa Library since the OS does keep record of the file type that can (and should) be used by applications.
A fix to this in the code is that under OSX, the Cocoa Library file methods should also consult the file type - given that many programs on OSX may happily save without explicitly using an extension in the file name.\
Flash (which didn't yield this problem) may have additional code to ascertain the filetype by seeing if it recognizes the data (given that Flash interracts with streammed data that would not have a file extension).