@the OP, it's supposed to be a Frequently Used Programs list, not Recently Used. Also, programs are tracked by Windows from everywhere, not just the ones opened from the Start Menu. For programs which run constantly (such as those which load at startup), Windows increments their run count by 1 per day. You can add a "NoStartPage" value as described here: http://support.microsoft.com/kb/284198 for the program you don't wish to see in the list again. Dunno if Start8 supports that system value, does it Neil?
We do not currently support that value, but I will make sure 1.1 does.
Regarding the MFU list order, we have selected weightings to the various values that we feel provides a good list order, but obviously different implementations may set a preference to one value over others. The inclusion of Modern UI apps also influences this somewhat.
Our job isn't to copy the Windows 7 start menu exactly, but also improve it where possible and thats why we sometimes do not produce the exact same results.
One area were we improved things is drag & drop from the all programs list. Under Windows 7 if you want to drag an item to the pinned item list from the all programs tree you have to drag it over the back button, wait a second or two before it switches mode and then drop it. With Start8 you can simply drag it to the back button and drop it and it will be pinned to the list.