My floating transport panel opened every time I started Cubase (not any more as I now use the lower transport in CB9). But, I suggest that you look at the Cubase>Preferences>General menu and change the setting for “Open project in last view used” to “Always”. By selecting “Always” Cubase will always open in the last view saved before closing. So if saved with the floating transport panel showing, Cubase will open with it showing. Be aware that this setting does not mean that every separate project will open the way they were saved. It means they will open the way the last one was saved.
Weird wild stuff for sure as it relates to opening projects but… at least the transport will be open if it was open during the last save. What the???