Note 1. Compressing the registry, especially the SOFTWARE hive may take a long time. It depends on the size of hive. Please wait for at least 5 minutes to complete the SOFTWARE hive analyzing. But usually it takes 1-3 minutes. If you see a HDD lighting while compressing the registry then all works normal, please wait for finishing.
Note 2. When registry files are being defragmented, the system takes 100% CPU time to finish it as soon as possible. This gives a chance to the registry not to be modified by any other program in the middle of the process. That seems as the system is frozen. You cannot stop the registry defragmentation while a registry file is in process. RFA can stop only after a current registry file is defragmented. This may take several minutes depending on your computer speed and a registry file size.
Note 3. Sometimes re-building a registry file increases its size. We are not sure what is the reason for that. The guess is: the original registry file has some data portions not aligned to blocks for fast reading/writing. Re-building the registry sets all blocks equal and this increases the file size.