Are those skipped times by any chance the same time it did a WU upload?
I upload to WU every 10 minutes, with an offset that should not interfere with my regular webpage uploads... but I find that very often the uploads to WU are not exactly at 10 minute intervals...
So I suppose if it got off schedule enough, it could interfere with a Weatherlink upload...
Also, just for "fun", instead of uploading with FTP, try writing to a local file instead, and up the frequency to every 5 minutes--see if that stops working, or if it collides with the WU upload...