Why is Merge into single pdf using InDesign CS3 and not CS4 ?

Question

I'm new to this so the question may be trivial, but it beats me:
I've created some InDesign files in CS4 and want to combine them into one PDF. So I opened Acrobat 9 Pro and
navigated to "Merge files into single pdf". I chose the CS4 InDesign files to Add and clicked the Combine Files button.
BUT, this starts up InDesign CS3 and not InDesign CS4 and returns a pop-up saying "unidentified error".
Why is starting CS3 InDesign and not CS4, and what is the "unidentified" error ! ?
As background I intially installed CS3 and then updated to CS4, leaving the CS3 applications intact. When I initially
bought CS3, just before CS4 was released I may have created pdfs from InDesign as an experiment, but it is possible I have not done this
since upgrading to CS4.
Thanks for any help

Answer 1

Thanks Michael, I was not aware of quality issues. Actually this is not really significant for my usage this time. What I'm doing is just using ID to capture notes/images/links etc in several free format ID documents. I then planned to merge them quickly into one pdf using Acrobat. I can easily shuffle the file order around to create a handy portable pdf reference document with the Merge feature.
Doing something similar from ID seemed to me to require me to create pdfs for each ID doc and them to merge them in Acrobat. I did start to write a simple script to do this in ID, but I then realised that I wanted the ordering to vary and the ID files would likely to change. Then I found the merge and bingo, that solved it..... Well it solved it on another CS4 installation that had never seen CS3, but not on my machine which had been upgraded from CS3.
I tried looking in the registry for obvious entries that might point Acrobat to use ID CS3 rather than CS4, but couldn't spot anything. I wonder if there is something buried in there ?
Thanks again for helping
Regards.