You may get N/A when it doesn't make sense to report a particular number. For example, if you've sold everything, %Gain will be N/A. Yield can be N/A depending on your date range, and yield interpolation range settings. It doesn't matter how you get your data into Fund Manager (manual entry, importing, retrieve), as long as the recorded data makes sense for the figure you're asking for, it will be reported.
To look into one closer, look at the equation for %Gain in the online help. Select "Help / Help on Report..." while you're looking at a Performance report. Look at your recorded transactions for a certain investment, and look at the date range of your report, and see what you would expect it to report. If you would like help. please post an example, as in what transactions are recorded, and what date range you're looking at.
I could not reproduce a problem with the sub-total option in reports. Can you still reproduce this? What report type are you looking at, and what "List By" option to you have selected?