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I noticed random inputs on netplay start when implementing GameYob's multiplayer into Cave Story DS, and this commit should fix it.
Unfortunately I can't test this as I don't have two flashcarts, but I can confirm that this did fix the desync problems I was having during early multiplayer testing.
There are a few more improvements I'd like to push as well (same frame delay on client and host, don't disconnect when packets aren't received, set SRAM transfer packet to require acknowledge), but I think this is ok for now.