For anyone else with this problem, this is what I do after every retune/reinstall:
Open SQL Server Management Studio Express and go to - Databases - TvLibrary - Tables - dbo-TuningDetail, open it, go to the lines for BBC THREE and CBBC Channel and set the pcrPid to 241 for both of them (one will already be 241, which one depends on whether you tuned before 7pm or after), find BBC Four and CBeebies and set the pcrPid to 201 for both of them. Now you have all 4 channels.
Open SQL Server Management Studio Express and go to - Databases - TvLibrary - Tables - dbo-TuningDetail, open it, go to the lines for BBC THREE and CBBC Channel and set the pcrPid to 241 for both of them (one will already be 241, which one depends on whether you tuned before 7pm or after), find BBC Four and CBeebies and set the pcrPid to 201 for both of them. Now you have all 4 channels.