ioFTPD can execute your program on event OnUploadComplete.
Code:
[Events]
OnUploadComplete = EXEC path\to\your\program.exe
...
in this case ioFTPD will pass next arguments to you program:
Code:
phisical\path\of\the\uploaded\file
CRC32 sum of the file being uploaded
virtual\path\of\the\uploaded\file