I think I might have to eat a bit of humble pie here regarding the subtitles bug 
More investigation makes me think it is to do with my SATIP feeds. Some of the channels have 2 types of Subtitles, DVB and Teletext. I only ever want the DVB ones so have been leaving out the PID for the Teletext stream in my SATIP configuration. Initially this missing stream turned out to be what was caused long tuning times, but the team fixed that issue in this beta.
However, what I hadn't realised was that the system still behaves as if there are Teletext Subtitles available.
In the Quick Guide Options display these channels show 2 lines under Closed Captions:
English
eng.eng
So this is what I now think is happening by looking at what happens to the tick boxes.
First Toggle Subtitles - turns on DVB subtitles - this works fine and DVB subtitles are displayed and the "English" has a tick by it
Second Toggle Subtitles - no subtitles are displayed so it appears to have turned subtitles off but it has actually switched to Teletext subtitles and the Quick menu options shows "eng,eng" ticked.
I'm not sure why it then switched back to DVB Subtitles again when I switch channels, maybe Subtitles state is only stored as a boolean not as which version of subtitle is being displayed?
For now I have added all the Teletext Subtitles PIDs back into my SATIP config so when I toggle Subtitles I now get:
First toggle DVB Subtitles
Second Toggle Teletext Subtitles
Third Toggle Subtitles Off
So when Subtitles are off they really are off.