It wasn't really designed to run in the standalone Flash player, as on the web you can disable those back/forward actions. I think... It's all so long ago I'm not sure I'm remembering it correctly now!

I originally built it like that for simplicity. I just use the Flash editor to move things around, position walls, graphics, interactive elements etc. You can set it up in a way that costs virtually no extra SWF size to have those redundent rooms, then you can map and plan the game as you go

I'm not really sure what "secret room" you're referring to. This is every room in the game. The empty ones are usually just inaccessable without the next-frame glitch in the video. I've had a quick look through, and I think every room that has content in it is linked in the game.

I found the old Flash project... The map works as a big timeline, with each frame being a room. It's 200 frames, 20 frames for the first row of rooms, 20 for the next etc. The following picture should make this clearer

I'm the original developer/designer of this game (I made it under contract to Aardman). I can probably dig out the original source and look into it if you like?