Disk Cleanup is a utility file that's built into Windows to clean up temporary files left by programs or files that you were working on. If the file is open or not in use, at times Windows plays it safe and doesn't delete them.
If you want Disk Cleanup to always cleanup your temporary folder here is the registry tweak to do this.
I caution you tweak your registry at your own risk and follow the instructions below.
Instructions:
Navigate to HKEY_LOCAL_MACHINE\ SOFTWARE\ Microsoft\ Windows\ CurrentVersion\ Explorer\ VolumeCaches\ Temporary Files
Locate and double-click on LastAccess. When you see the Edit DWORD Value dialog box, change the Value Data setting from 7 to 0 and click OK. Setting it at 0 will make Disk Cleanup Tool delete all the files. If you set it at say 1, it will not clean the last 1 days temp files.
Link
If you want Disk Cleanup to always cleanup your temporary folder here is the registry tweak to do this.
I caution you tweak your registry at your own risk and follow the instructions below.
Instructions:
Navigate to HKEY_LOCAL_MACHINE\ SOFTWARE\ Microsoft\ Windows\ CurrentVersion\ Explorer\ VolumeCaches\ Temporary Files
Locate and double-click on LastAccess. When you see the Edit DWORD Value dialog box, change the Value Data setting from 7 to 0 and click OK. Setting it at 0 will make Disk Cleanup Tool delete all the files. If you set it at say 1, it will not clean the last 1 days temp files.
Link