Lalibgal congradulations on your purchase and welcome to 6MT.net. I am sorry to hear about your rust problems, but there may be a related issue to your car.
This topic is about rail dust:
http://www.6mt.net/forum/topic.asp?TOPIC_ID=7356
What I would suggest is that you take your car into several (at least 3) reputable autobody/paint shops (not Earl Scheib or Maaco). Ask them for their opinion on what might be causing the problems and what it might cost to repair the problem. Be careful because some places ask a non-refundable deposit for quotes. Personally I would not give my business to such people. A reputable company should be able to give you a free repair quote (this is very minor time to produce a quote as the repairs are simple) as it should be part of their normal overhead costs.
The paint is a sore issue with the Nissans. Due to changes in environmental laws the paints have been changing so the more durable paint used on your Civic is not the same type of (more environmentally friendly) paint on the G's. Due to the less durable paint many G owners use clear bras (use search function and you will get numerous threads for this) to help protect the front of their cars as that is where most of the damage due to chips will come from.
What this means is that if your roof paint is chipping you should be able to see the chips and if caused by road debris you should see numerous chips to your hood, front bumper, etc. If it is indeed chipping and is only to your roof, you might want to look at what you are parking your car under. Could be a rusty pipe at your apartment or work garage that is transfering the rusting materials to your car.
Good luck and let us know what the problem was.
"you will rue this day....well go on start ru-ing" Stewie Griffin