A wild guess: Since you reopen FILEOUT to a new file without closing it first, maybe there's an issue with some buffered data ending up in the wrong file? I think perl is usually smart about closing file descriptors in cases like that, but I don't know if you can always count on it. Perhaps you should close it before reopening it.

reopening a file handle to a different file is just fine. I/O Buffers do get flushed to the disk and the file is closed in the normal way. You can do an explicit close(), but it is not necessary.