any thoughts on this ?
It's possible the sysprep reset your administrator profile. I haven't seen it but possible. Either that or you have re-directed desktop setup in your GPO. Many times people do this so the desktop, Mydocuments, My pictures, ect are redirected to a network share location so users think they are saving to their desktop, but in reality they are saving it onto a server location somewhere that is backed up. Also this way anytime they login somehwere their desktop goes with them. Not quiet roaming profiles but more mobility. Was this setup at all?
Try putting your files in the C:\Users\Default\Desktop, re-create the template and deploy it letting VMware sysprep it with the customization wizard, see if that fixes anything.
What desktop version are you working on with this problem, WinXP, Win7, Win8, Win8.1?
I am doing this test on Esxi 5.0 U2 and with a windows 2008 R2 server. The files I saved on desktop, I saved same on C:\ directory after sysprep desktop files were gone while in C:\ directory I found them as it is after sysprep
So, as you are saying it is re-setting administrator account what if I have another account like 'user a' and have some files on that user's desktop, they will also go ? sysprep will also reset that account ?
The files I saved on desktop are doc files only.
If you put the files in the default user account, its hidden and found under C:\Users they should stay. The default user account is like the All users account back in XP. Anything on the Default users account's desktop will show up on ANY and ALL users profiles desktop.
Give that a try
I found the user defined account wound not be removed during guest OS customazation, but not sure if the files related to it will be removed or not.