You log states you are using CS5.5 - 7.5.0 so you might want to try the latest available update (7.5.2) at http://www.adobe.com/support/downloads/detail.jsp?ftpID=5275
It may not help the problem but I guess it's worth a try.
Try disabling the live preflight as well to see if that helps the performance on taht particular document at least.
I'll give it a bash - I wasn't aware of patch.
The ID files I am working on are within a Dropbox folder.
Try working on local disk for a while and see if you can replicate the problems there.
Thanks for the feedback.