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I did also have this problem which happend when i went from 8.8 to SP1 - I've applied Service pack 2 as suggested by Support and the issues have gone away.
It was taking a minute to has the files, so in one of my deployments i had 800 odd files...so was taking a very long time before it even started doing anything!
I would log a case
It seems to have raised its head again - just tried using the same job but using HTTP and its taking ages to hash and gets stuck on 1 of the files :(
I had a similar experience with Office 2003. What I did was to change the "Run from source" option in Delivery Method to "Use Multicast". The thing is that it seems that LANDesk network efficiency is very low when using "Run from Source" or "Download from Source" options.
I have the same thing.
Apparently its a normal part of the process. The good news is it only does it once, unless you change your package.
Logged a call with LANDesk and they provided a patch, which fixed the problem.