SdFat: Why does the first write to the file take so long?
Most file systems exhibit poor performance if you store many files in one directory. 'Normal' desktop computers are perhaps so fast, that you don't notice the performance impact, but accessing the file system from a relatively slow micro-controller, which also have limited means of caching the file system data structures in RAM, you may have to consider for this and either write a smaller number of files or build a tree of directories, so that you only have a limited number of files in each directory.