Here is what I do:
1) Setup all options the way you want it.
2) Open up RegEdit. Navigate to HKEY_CURRENT_USER\Software\VB and VBA Program Settings\CCleaner\Options
3) Export that key to a file (i.e. CCleaner.reg)
4) After the installation, you can double-click and update CCleaner with those settings, or script this update
This seems to work across all versions of the program, we started this back in Version 1.2x. Also seems to hold if you upgrade.
Happy Networking,
Chris