After creating a texture pack last night, with animated textures, i uploaded it as i always do to my server, and when i restarted to test it, all the textures were off and none of the animated textures show, only display "Missing Texture" it worked perfectly in 13w07, i dont know whats wrong or how to fix
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This is different, however. this cannot be fixed as the other bug can, as it is a server problem.

The server does not play a role when handling texture packets except for providing the download URL, the rest is handle by the client.
Did you follow the instructions in the changelog for 13w09c ?
Animated blocks and items in texture packs now requires the animation definition (previously it was optional)
if by animation definition you mean the blockname.txt then yes, it works fine when i test in my client on this, however it doesnt work on my girlfriends computer with the same exact files, zipped or unzipped.

Please update to 13w09c, since MC-10355 was fixed there.
Duplicate of MC-10355, please use the search function to see if your bug has already been submitted. Currently over 53% of tickets are being closed as duplicate.