GBC with SGB border =
 Works only if game has both SGB and GBC features (or system type is set to GBC).
 Emulates both SGB and GBC at the same time. Doesn't work with all games.
 (Use GBC with initial SGB border option in that case)
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 GBC with initial SGB border =
 Emulation is started in SGB mode. When the border is uploaded it resets to GBC mode.                Â
 To show border in games that have "SGB feature: no" in ROM info, but can show a border
 (Pokemon Diamond, Pokemon Crystal,Wetrix GB) set system type to SGB and this option on.
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 Will affect when resetted (or rom is loaded)
From my understanding, the previous beta versions supported only the first mode to get both GBC colors and SGB borders working, which only worked for some games, while this latest version works with the second method as well. My conjecture for this is based on the following quote by Dwedit on PocketHeaven that he made about a day before this latest release:
Dwedit
Next release will be able to add SGB borders to SGB/GBC games.
How does it work? It checks if the game supports both GBC and SGB mode, then runs it in SGB mode for about 1 second until the game adds its border, then reboots in GBC mode. Some games don't like this, because they only add the border after you begin the game. Those games won't get a border.
When it's running in SGB "border add mode" for ~1 second, the game is disallowed access to the save ram. This is because games like Conker's Pocket Tales and Warioland 2 offer to delete your save game if you boot them in a regular gameboy and a color gameboy save exists. So all the games see a blank save for that 1 second, then load the normal save as it reboots in GBC mode.