The in-game timer counts active frames (assuming 60 per second) but it skips lag frames spent loading graphics data between screens. It also halts if you pause the game, and stops when the ending sequence is triggered.
You can turn the clock on in the PC build to see the timer overlaid on the screen. That will show you when it starts and stops, the NES version behaves the same.
On the PC the lag frames between screens are always the same, I think it's always 20 frames from room to room. On NES it varies depending on how much graphics are shared between rooms, seems to take either 19 or 20 frames in most cases. The exact number of frames depends on the route.
Also, the NES is usually close to 60.1 Hz, and the PC version runs at 60 Hz. I think that's about 2 seconds over ~20 minutes.
So, the two platforms are designed to be frame-for-frame compatible while you're able to give input to the player, at least. The in-game time is just a frame counter and should give equivalent times for frame-equivalent runs. Real-time though I'd only expect a difference of a few seconds overall.
For testing the NES ROM, here's a LUA script that works with FCEUX that will display the in-game timer. You can see exactly when it pauses with this.
Looking at two recent times using the same route, comparing NES to PC:
Smartball: 19:02 real time, 17:31/13 game time (NES) ChoaslegionKaeru: 19:20 real time, 17:45/59 game time (PC)
So we've got 15 seconds from the in-game timer, and 18 seconds in real time. The 60.1Hz vs 60.0Hz difference accounts for about 2 seconds, so that leaves 1 second unaccounted for.
As I said in the previous post, the game's timer does not count pauses (dialogue, etc.) or lag frames during the room transition. From these numbers I think the average NES room transition is a little bit faster than the PC. (There's no exact
So, as a rough ballpark, I'd estimate the PC loses about 0.15s per minute versus the NES.
ChoaslegionKaeru switched to the emulator version, but just as a point of verification: he recently timed an 18:43 with 17:14/23 on game clock, compared with Smartball's non-emulated 18:43 with 17:15/03 on the game clock. So, all other things being equal I think that's good confirmation that the emulated times are directly comparable.
