Hmmm, then for once your guess is as good as mine. I did a quick double check on my system of all combinations of single/multi user installation both logged in as an administrator and logged in as a non-administrative user. I used version 2.6, but this feature hasn’t changed since it was added to PDFClerk, so the version should not matter.
I’m not sure what particularities your system may have that prevent the installation. What system version are you running? Is FileVault turned on, or any other form of encryption or security? Any other particularities that might have an influence on access rights? And, just in case, what model is your Mac?
In any event you can install manually by putting an alias to PDFClerk in one of the following places:
For single user: /Users/<yourusername>/Library/PDF Services/ (i.e. inside the Library folder in your home folder)
For all users: /Library/PDF\ Services/PDFClerk (i.e. inside the Library folder at the top level of your system disk)
I hope this helps.