I think I have discovered a new bug. I found out what the issue was but had to perform a factory reset in order to cure it. Here's what I think cause the issue.
I have Big Brothers Little Brother on series link for channel E4. On Sunday's it is first aired on T4 on channel 4. Last weekend because I was going to be out when it was on E4 I set a one-off recording for the T4 airing on channel 4 (as I was going to miss the start if I didn't). Obviously the HDR recorded this showing and also the series linked showing on E4 later that afternoon. Thinking about it (and confirmed by checking this weekend) the PROG CRID is the same for both showings but the SERIES CRID is obviously different.
Now whilst playing around trying to set the F1 race and getting recording clashes I discovered that attempting to record channel 4's showing of BBLB on T4 resulted in it asking me if I wanted to cancel the series link. Now that was very odd because it was not in my schedule and did not have the clock symbol in the EPG. Confirming that I did want to cancel it cancelled the series link for BBLB on E4.
At this point I successfully set a recording for the F1 race however I then could not set a series link for BBLB on E4 nor CH4 with it complaining of a clash. Cancelling the F1 race scheduled recording then allowed me to schedule BBLB on E4 however it was still linking itself to the channel 4 (again not in the schedule and no clock on the EPG) and I could not set the recording for the F1 race.
Because of this very odd behaviour I decided to perform a factory reset and now I have managed to successfully schedule my Sunday afternoon recordings. I'm pretty certain there is some weird crap going on here where it seems to have got itself all confused by forcing it to record a program with the same PROG CRID twice but with a different SERIES CRID. It's the only explanation I can think of.
If anyone's bored feel free to investigate