As far as I'm arare of, the MP4 downloads on BBC iPlayer only work with BBC's own desktop player utility, as it uses Adobe Air's DRM.
If the programmes you are after are still on the iPlayer website, you can try getting them with the utility get_player. What this utility does is record the stream version (which is DRM-free) and outputs an MP4 file which can be played on just about anything that supports MP4 files with the H264 codec. The utility is command line based, so will take a little while to get familiar with the commands.
To download get_iplayer, click the last link in the 'Download' section of this page. During installation, it automatically downloads and installs a set of plug-ins for it to work.
When you run get_iplayer, the first thing you do is type in get_iplayer, followed by a word or two from the programme title, e.g. "get_iplayer click" if you're after the Click programme. It then displays a list of titles and dates with these keywords, with a number to the left.
To record a title, type in "get_iplayer --get ### --modes flashvhigh", replacing ### with the number that appeared next to the title of the programme you would like. If the programme is in HD and you would like the HD version, replace 'flashvhigh' with 'flashhd'.
Once complete, you'll find the resulting MP4 file in "iPlayer Recordings" on the desktop. This file will play in anything that supports H264, e.g. VLC, USB port of most newer TVs and so on.