I have had the same problem with my polar express, which i just bought recently. Having to send it to the USA from the UK would be very expensive so i decided to open it up myself. The tamper proof screws were a bit of a problem getting into it. I ground down an old screw driver into the triangle shape to undo them. I then replaced them with self taping srews the same size.
The Problem I found was simple, there is an internal (250V, 8Amp) fuse soldered onto the red wire on the secondary winding of the transformer. The red wire going from the transformer to the PCB, the fuse has black heatshrink over it.
There is no room inside the housing of the controller to fit a fuse holder. I fitted a box on the side of it with a panel mount fuse holder. drilled a hole through the housing, fitted longer red wires, so they could go through to the terminations on the back of the fuse holder.
At least now I can change it simply if it blows again.

hope this is of help to you.

Inside the unit is an 8 amp fuse, connected between the transformer 16V output and the electronic control board. This has probably blown. Seems quite a common fault.
If you can remove the four fixing screws with special heads that hold the top and base together, you can replace the fuse.
I had to drill the heads off these screws, remove the studs after filling flats on the and replace with standard screws.
I replaced the fuse with a 4 Amp polyfuse type RUEF400, (which resets after you unplug the unit for a few minutes) but you could drill a hole in the case and fit an accessible fuse holder.
The fuse shouldn't blow, because the overload cut out should prevent excessive current in the event of a short circuit, but maybe some units operate at too high a level.
CAUTION: Do not remove protection, the transformer could overheat and catch fire.

You can get the correct triangle screwdriver from amazon.com at
http://www.amazon.com/Silverhill-Triangle-Screwdriver-Roomba-Happy/dp/B001F3FUBK/ref=sr_1_1?ie=UTF8&s=hi&qid=1277110784&sr=8-1-spell

Byron

I did the same thing as brian-sw. Opened the unit, removed the old in-line fuse and added an external fuse holder to make it easier to replace in the future. Transformer is difficult to open unless you have the triangular security screw driver. Security bits can be purchase from Harbor Freight but you will need to adapt them to fit into the channels where the screws are recessed. It certaintly would have been nice if Lionel installed an external fuse or circuit breaker. Guess they didn't want to loose the repair business.

Just a suggestion....if you're looking for the fuse....it located in the corner of the case under the green light. I used a dremel tool and cut a 2 inch access into the case to access (on the side of the rear corner not the top) the fuse since I was unsuccessful at finding the screw driver. I snipped the wire at each end of the fuse and replaced it with a 250V 8amp fuse (and heat shrink covering and a fuse holder for future access). I had a plastic body from an old toy that I used to make a removable cover from too.

Sounds like the problem has been properly diagnosed, maybe I can help with the tools... Harbor Freight has a very nice and fairly complete set of security bits for about $12.99

I contacted Lionel Customer Support. They are sending me a replacement transformer at no charge. I suggest that you do the same.

SInce my transformer was out of warranty, I found a Lionel certified merchant who replaced my transformer with a brand new one for $29.
BTW, I had a Lionel dual crossing gate fail after about 5 times around the track. I called Lionel and they are replacing it for free since it was new and under warranty. I would recommend all of you contact Lionel first with this problem, they may make you whole without much fuss. You can find the customer service number at lionel.com.

Sometimes when the green light blinks, the track has just come apart. Unplug the transfomer and check all the tracks. Make sure the locomotive and the rolling stock are all properly alligned with the track. Plug the transformer in and give it a go.

Our train did the same thing. The solution was to wipe the track down with a wet cloth and clean it. The track was dirty and all of our problems were fixed!!!! The train connection were also dirty with dog hair. Easy fix hope it works.