I found this on FF:- (so why do they give you the option to adjust then??!)
When I wake up at a different time, should I adjust my temperature?
We are often asked whether temperatures should be "adjusted" when not taken exactly at the same time. Some simple formulas are sometimes applied to adjust for differences in waking time. We are often asked whether this is accurate or not and if it is worth correcting the chart.
We recommend against adjusting temperatures as in general the resulting temperature, though it may be more pleasing, is not more accurate. The reasoning behind our recommendation is based on the fact that the Basal Body Temperature variation with time is dependent on your own unique metabolism. While most women see a difference, some women do not see much dependence of the BBT with time and can live with a variation in time without masking their pattern. For many others even a 10-20 minute difference will have strong effects on their charts. Similarly, some women see an increase of their BBT with time while others may actually see a decrease. From the diversity of the charts that we have seen, it is quite clear that no simple generic formulas will be able to compensate for time differences.
Our advice is to use an alarm clock if necessary to try to keep the time as constant as possible. If you have an occasional waking time difference, just record the time but leave the data as measured and make a note if there are unusual circumstances. In most cases our software should be able to see your ovulation pattern despite a few inaccurate data points.
If you have inaccurate data points that are causing you to have an invalid or confusing interpretation, please ask for support to help evaluate your chart.