Broken animations

We have simple 2D game with animations. We have problem with sharing source code and switching platform which results into missing transition animations. Object disappears until final state is reached. We have tried sharing via Dropbox, git (with .gitignore) and mercurial (with .hgignore). What works is compressing whole project to zip or using mercurial without .hgignore (so our developer commits whole Library folder, which introduces problems to collaborative development). If I delete Library folder, then animations breaks. Currently, we are developing for Android. We would like to build our game for Windows and iOS. But, when I switch platform to Windows, animations breaks again. If I switch back to Android, they stay broken. I have tried set visible meta files. Thanks for help.