In my latest run, I noticed that the in-game time for my save files throughout the run were about 2 minutes slower than the real time; as it turns out, IGT tracks time on the menu, in addition to time spent actually playing the game. It does this when stalling on the screen at the end of a run, too; any time spent just sitting on the end screen is added to real time. This might be a solved issue already, since mardek 3 doesn't use IGT, but the leaderboards here default to IGT for their rankings. I'm not sure how to accurately find the in-game time for my run, so I've just put it in with the difference between IGT and real time from my last completed run for now.

I'm not totally certain what you mean, menuing is a part of the run, so time in menus should be counted -- the timer does keep counting during the end screen, that's why it's vital that you save as early as possible. That said, I've no issue with switching to RTA, since reloading is an integral part of the run.

There's a tool I wrote to get accurate IGT out of a save file: https://github.com/jbzdarkid/Random/blob/master/mardek_sol_reader.py thought I'm not sure what exactly your concern was. 3 is not using IGT because reloading is extremely required. But with the geojacket skip, I feel like 2 has similar requirements, so I've changed the board.

Oh, I don't mean the in-game menus, that's definitely integral to the run. I mean the main menu; before starting the run I just sat on the main menu for a while, and it ended up offsetting the in-game time by several minutes in addition to the 30 seconds I spent on the end screen before saving. The IGT tool ended up returning 40:35, which is way over what it reasonably should be. I'll have to be more careful if I return to this category in the future with saving at the end, I didn't know that it did that.