What type of frequencies are programmed in? Commercial/public safety or ham? If the latter, have you stopped scan, put the radio on one frequency and keyed up a transmitter nearby (handheld works nicely if you don't have a service monitor) to see if the radio hears it? If it hears a weak signal, then that steers you to scan programming instead of frequency programming. If not, are there subaudible tones set for receive (CTCSS, DCS, etc)?
What software are you using? Give me the Rev. level. I hope you are using the older level and not 3.0 s/w. 3.0 s/w will not allow wideband so ham programming is out of the question unless you went to an Icom dealer and got the "exception" document that allows wideband.
Have you tried programming a ZONE, and then putting all 7 weather channels in it and enabling SCAN? It should stop on the first one it can hear. If you have more than one that the radio can hear, you can cycle thru them.
Provide a little more info and it will help narrow this problem down.
Bob