Actually, if I remember correctly, the issue is more the types of files. The MS installer seems to be geared towards supporting executable, DLL and similar files really well, as in only needing to check the file checksum (stored somewhere in the file) to determine which files have changed and need to be updated. Calibre hals almost no such files, so the installer has to actually compare each pair of files completely to determine if that file needs to be updated.
Anyway, the bottom line still is to wait until that stage finishes
