There are several possible things you may need to look at. First off, any issues or queries with MyStuff are best addressed at
http://forum.toppy.org.uk/forum/viewtopic.php?t=5735, the forum for the current version of MyStuff (4.54, currently on 4.54e I believe).
Otherwise, check the following:
1. Does your MyStuff EPG show those programmes as lined up for recording (a red 'C' or 'R' in the corner of the programme)? If there is an exclamation mark (!), there is a timer clash. No mark means nothing is expected to record.
2. Can you see the timers in the timer lists?
3. Are you using ControlTimers to pick up the series automatically?
4. If so, have you checked the search criteria? A common problem is an Exact Match when there is a space at the end of the search string; for example, "Gadget" is not the same as "Gadget ". This is easily done if you set it up manually.
It's important to know whether or not your problem arises from the timer not activating, the box not waking up for a timer, or from a MyStuff ControlTimer set slightly wrong. If all else fails, try a cold reboot.
With CTs too, in the ControlTimers lists, it tells you how many programmes it has lined up for recording. Use the white button (and FF or RW if necessary) to see existing CTs.
Uninstalling MyStuff shouldn't make any difference, normally. Once timers are set the PVR takes over the recording.
Hope this helps!