It can take 4.5 times or longer to process in UnSafe Mode rather than in Safe Mode. In UnSafe Mode the InnoScript has to search all the folders that are available to find another copy of the file it was supposed to find in the system folder.
So if you do not have these files in a folder readily available to InnoScript it could virtually search the whole disk for each file in question. This is why we recommend that you place these files in a seperate folder (after verifying that they are safe to deploy) and let InnoScript know where they are (add to beginning of Search Path).
Safe Mode searches will find the files much quicker because InnoScript will look in the system folder for every dll/ocx/exe first, and will find most of them there.