Recording from the guide (or EPG) uses something called "alternate instance" which always chooses to record the original / first screening of the selected programme.
The recorder would see the same programme on the Plus 1 channel as being identical to the one on the original channel and would always opt to record the show on the original channel and skip the one on the Plus 1 channel (unless there is a prior conflict in your booked recordings).
The advantage of recording off the original channel is that broadcast quality is often better, leading to better quality recordings. For example, most prime time shows on TVNZ 1, TVNZ 1 and Three are broadcast in HD via UHF; while the same shows on the Plus 1 channels would be broadcast in SD.
However, if you do wish to record from the Plus 1 channel, you can do so by manually setting the timer. Please refer to your device manual for instructions on how to do this.