The PT 2007's Registry Cleaner is slower than PT 2006's because PT 2007 uses new scanning engine that is slower but produces much higher quality results.
PT 2006 and every other registry cleaner on the market (AFAIK) analyzes the registry one piece of data at a time and treats all data as separate entity.
For example, lets say there are the following erroneous registry entries in your registry:
Erroneous data1
Erroneous data2
Erroneous data3
Where Erroneous data3 is the "main error" that causes the entries 1 and 2 also to be erroneous.
PT 2006 (and every other registry cleaner on the market) would attempt to solve the problem by first attempting to fix the Erroneous data1, then the Erroneous data2 and finally the Erroneous data3, one by one. If a fix is unavailable the best fix is determined to be the removal of the data from the registry.
Thus, in this case, the Erroneous data3 is fixed and Erroneous data1 and Erroneous data2 are deleted from the registry.
But PT 2007 is the first stateful Registry Cleaner. It means it can analyze that all three errors are connected and attempts to fix all of them as a whole. When it is able to fix the Erroneous data3 it knows that Erroneous data1 and Erroneous data2 are no longer erroneous because the root cause of the error (the Erroneous data3) was fixed.
Thus, in this case no data is removed but all three errors are fixed.
So, in English: PT 2007 does a much better job in fixing registry errors.
Therefore the question is whether you prefer speed over quality. If you like speed, you can just use PT 2006, it's a very good Registry Cleaner. But, if you prefer quality you should select PT 2007, it's better.
We are working hard to make the Registry Cleaner faster for PT 2008. It's also possible that we will add an option to PT 2008's Registry Cleaner window to allow the user to select whether the cleaner should emphasis quality over speed or speed over quality in the scan (i.e. whether to use the stateful analyzis or not).
