CryptaPix 3 can view and decrypt CPX files made with previous versions (with the proper password, of course). However, CPX files created in version 3 cannot be used with earlier versions of CryptaPix.
No, each program uses a slightly different pixel shuffling routine and Puffer uses its own PUF file format internally.
First place the files you want to compare into the Image Bin. To look on an entire drive, select the root folder for that drive in the File Manager and then select "Add all files + subfolders to bin" from the Folder menu. This may take several minutes. Then select the Image Bin tab to view the list of files in the bin. Now make sure "Show CRC values" is checked on the Bin menu. Once all CRC values have been calculated, click the CRC header to sort by that column. Finally, select "Group sorted data" on the Bin menu. Files with the same CRC value will now be group together at the top of the list.
There is a compatibility issue with older versions of DirectX. Make sure your DirectX drivers are version 9.0c or later.