Ah, now that's good info. Thanks! B)
Yeah, I forgot about the possibility of the 16-color EGA mode. That would explain perfectly why there are 2 EGA palettes in the VGASPEC file, but just one VGA palette.
I'm not totally familiar with all the details of the EGA, but this is what I think is the case here.
The EGA is complicated partly because it tries to accomodate many possible configurations of hardware. Its vidoe memory for example can range from 64k, 96k and 128k (or something like that), and it can either attach to the RGB monitors that the CGA uses, or a more advanced monitor specifically for EGA use.
The CGA monitor (often called an "RGB" monitor) only supports the 16 CGA colors. So an EGA attach to such a monitor would only be able to use those 16 colors, since the monitor physically cannot display other colors. So presumably the 16-color EGA palette would be used in that setup.
With an EGA monitor attached however, the colors displayable by the monitor expands to 64, so in that setup presumably the 64-color EGA palette would be used.
If I remember correctly, the EGA does not actually have a graphics mode (at least a standard one) that can display 64 colors simultaneously. This is where the concept of a programmable palette first appears. You can only display 16 colors at a time, but the EGA allows you to reassign the colors, so that at least you can pick which 16 colors to use.
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In Lemmings, for both VGA and either configuration of EGAs, the graphics mode used is actually the same, namely 320x200x16 colors. This is why there aren't EGASPEC files. The difference is in how colors are used. The VGA setting uses the VGA's palette mechanism which allows you to pick your 16 colors from 2^18 possible colors. The EGA setting uses the EGA's palette mechanism which allows you to pick from either 64 or 16 colors, depending on what monitor is attached.
Unfortunately it would probably be impossible to test my theory on modern PCs, since it would always be treated as an EGA+EGA monitor configuration when you try to talk EGA to it, so you won't be able to get an EGA+CGA monitor configuration.
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Oh yeah, on an unrelated note, an update to that doc of mine. In it I think I said I wasn't sure which method the game uses to decide where to place the 960x160 within the overall level area. Testing with myvgaspec seems to show that it always places the 960x160 bitmap at location x=304, y = 0 in the level area.