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Exoray
Trying to load that save prompts me to insert Disc 2, just as would be expected.

I think it's pretty clear that whatever version you are running now, it's not behaving like normal and thus can't be used for a run.
You're just going to have to use a full installation and skip the cutscenes manually.
Edit history:
WAZAAAAA: 2012-04-30 11:51:13 am
WAZAAAAA: 2012-04-30 11:49:17 am
WAZAAAAAAAAAA AAAAAAAAAAAAA AAAAAAAAAA
Understood, let's forget about the minimum installation once and for all. Damn you're too good at what you do SDA staff, haha. Thanks for all your patience and testings moooh.

The alternative to such run for me would be doing a flawless segmented-run (with the Full installation of course), but first I have to ask two questions and re-write an issue that went unnoticed.
1. Does the game prompt you to insert Disc 2 even with the FULL installation? That would be a waste of time
2. Can I decide if the final run can be uploaded in, let's say 10 parts or a single part with all the segments in it? A run that plays smooth like the Halo 1 would be awesome, but I guess that games with checkpoints are treated differently. If the video gets split, am I supposed to record the Menu screen for every segment?
3.
Quote:
BUT, I have an issue (yes, another one) when recording the pause-menu with Fraps. Take a look at 1:02:53 of the video, when I attempted to use the bug by loading the empty savestate and skip the fight. It won't record the menus because apparently they're not recognised inside the game for Fraps, and as you can see from the top left of the screen, it shows the glitched FPS counter. Not sure if Dxtory does the same thing, but how am I supposed to show that I actually save the game in case I wanted to make a segmented run otherwise? Is that necessary?
Confirmed for Dxtory having the same problem. You should test Fraps and try recording the pause menu to understand.
Exoray
1: Probably, but it doesn't matter since disc swapping never counts towards your time.
2: It's common to append a segmented run into the same video file to make it easier for the viewer so that shouldn't be a problem.
3: A common issue when it comes to older pc games, fraps requiring hardware rendering and most of the times menus were done in software rendering. We'll probably end up adding a small generic token time to compensate for each access to the menu. You aren't going into the menu unless you are going to save anyways, so it should be easy to just add another second to each segment time or so.
WAZAAAAAAAAAA AAAAAAAAAAAAA AAAAAAAAAA
Can you please test number 1 for me?
Ok
And I'll see if I can fix it by changing Fraps/Dxtory and the game settings
Invisible avatar
The game doesn't ask for CD2 if you use full install, as I recall.