I'm not sure if it is the case for multiple HDDs, but if you partition one HDD, windows is only capable of recognizing each adjacent partition up until it finds one it doesn't recognize, and none after. Since Windows does not recognize Linux partitions, if it comes directly after windows and you have another recognizable partition, say a different version of windows, after it, it will not recognize either of them. This is possibly your problem. If you have Ubuntu at the start of your second HDD, Windows will likely stop looking as soon as Ubuntu is detected.
I can't guarantee results, but if you put the Ubuntu partition at the very end of the second HDD, you will hopefully be able to read the rest of it. Make sure that you make Ubuntu big enough for Ubuntu data to build up, as it is much more time consuming to add space to the start of a partition than it is to add to the end. That being said, Ubuntu is capable of reading and writing to any partition without ill-effect (except the occasional trash can folder and obviously files incompatible formats; no different than if you were to use a flash drive between the two), as long as you gain r/w permission for them. This means that you will only really need room for system files, you could very-well keep all of your personal files on your windows partition if you wanted to. (When I still used windows I gave it 100 GBs, followed by a large ntfs partition for shared data and the last 50 GBs to Ubuntu, and put all personal files on the shared partition so that they were accessible to both OSes).
Also make sure that the extra partition is in a format that windows is compatible with. I used to use ntfs because I also had Snow Leapard for a while and it is compatable with all 3 OSes, FAT would also work with all 3 (this is what flash drives use by default).
