exe files lost after XP Pro install+file/settings transfer

[btmf13]

I just installed XP Pro on my new hard drive. My old hard drive is installed as a slave containing all of my programs, etc. I used the XP app. that transfers all old files and settings from another computer to the current, and now all of my exe files seem to have been lost. If I open the Program Files folder all of the files are intact except the .exe's, and I think some .dll files may be gone as well. Of course I reformatted the old drive thinking everything was safely transferred. After I noticed the missing file problem I browsed the system backup I had created previous to the transfer, but this did not list the slave drive contents (even though I selected to backup everything). Did I lose everything, or am I just missing something??? Please help!! Thanks!