Part of the Root Cause Analysis (RCA) suite has a section dedicated to tracking transports between the various systems and even has a built in comparison tool for situations like you currently have. I have also recently learned that the time stamp on the transports is the time that they were imported into a system, not the time of the extractor running.
It even allows for the information to be exported to an excel sheet so you can quickly email out a list of outstanding transports.
Now for the caveat, you must have those systems already managed under the setup work center; not a big deal if you don't as I think a comparison can still be accomplished, but all the current transports are going to show up for the first day.
Here is an axample of a Dev BW system:
The green box is to show the excel export function, and the "Events From" is a date filter, you may have to choose a date to go back to in order for all the transports to come up.