Hey Chris!
This is a bug we’ve hit before in the FumeFX SDK. They expose a function that takes a file sequence name and does the frame substitution, but it seems to get messed up when the path has extra periods. Its even more annoying because they obviously don’t have this issue with the core FumeFX code, just with the function exposed via the SDK!
I’ll try using our code for filename stuff in the next version of Krakatoa (currently in beta), but there is no solution in any existing builds short of changing your filenames. Sorry about that.