What version of Wowza are you running?
Can you please confirm that your custom module is writing the FLV file to a specified directory, or if the file is being saved to the [install-dir]/content directory.
If you are running a Wowza version previous to Wowza 4.x, and the custom module is working as expected but not creating an .mp4, it could be because previous versions of Wowza recorded to .flv. You can specify the recordings be saved to .mp4 by editing [install-dir]/conf/Server.xml and change:
And change to:
If you are running Wowza 4.x, and/or your module is not working as expected, you could try the Wowza ModuleMediaWriterFileMover:
How to move recordings from live streams (ModuleMediaWriterFileMover)
I hope this helps.