with the news that BBC3 is going online only will that affect GIP's ability to download shows and series?

No, but there is no way to know for sure how things will work until the switchover. Given the way get_iplayer works currently, you wouldn't be able to search for BBC Three programmes or record them via PVR, but you should still be able to download them individually.

lwhilst the BBC3 progs do appear in the TV cache, however the two progs I am trying to download both fail to download. They both go direct to the command prompt.
cuckoo s3e1 and all the episodes of mongrels, I have tried with the PID and the program number.
Other progs on BBC3 will download without a problem. Any idea what could cause that?

Works fine here. If you don't post your command line and the output received, we're not going to guess.

(17-02-2016, 08:07 PM)Works fine here.  If you don't post your command line and the output received, we're not going to guess.

or
where xxxx= the programID

but other programs work with the same command and different pids or progid

One more chance - read my earlier reply again, carefully.