This happens when you are using the "Do not overwrite existing files"
option on an installation folder with a large number of resources. When this option is enabled on one of the installation folders/registry keys here it is what happens:
1. before the current setup is actually installing its resources a backup copy of the above folder/reg key is made
2. the current setup installs its resources
3. at the end of the installation the backup copy of the original resources are restored in the original location and they overwrite the installed resources, thus the original resources are restored
If the original location of the folder/reg key you enabled the above option has a large number of resources, then the backup and restore operation could be tedious. In this case please double check which folder/reg key you enabled the preserve operation on and if the preserve operation is not required by all their child resources, than try to enable the preserve option explicitly only on the child resources you need to be preserved.
Hope this helped.
All the best,