I agree with others.  Leave it alone, be consistent with what you do through this hatch, and analyze the results to see if you need to make any adjustments next time.  If you start fiddling with the controls and conditions, you will not know what to adjust to make it better next time, if you even need to adjust anything.
That model should be a forced air, so the temperature should be constant through out the incubator.  In a still air, the hot air rises so you will get different temperatures throughout the incubator, but not in a forced air.  I know you can have sheltered spots in some forced air incubators, especially homemade ones, but this model should not have that problem as long as the fan is working.  It is a good incubator.
Never trust a thermometer that comes with the incubator or any other one that you did not calibrate yourself.  They do not necessarily read true.  Two different reasons.  Some are just not that accurate.  The ones that are used to take the temperature outside are usually required to read within 1 or 2 degrees of the same temperature each time.  This does not mean that they are within 2 degrees of the correct temperature, just that they will return to within 2 degrees of the same reading each time.  For incubators, you need a thermometer that is supposed to read within 0.1 degrees.  Even with these, you don't necessarily get the correct reading.  You need to calibrate them.  Due to manufacturing tolerances, they may be off the real temperature.  To see what I mean, next time you are at a place that sells outdoor thermometers, look at them.  Thermometers on the same shelf in the same climate controlled conditions will often read 4 to 6 degrees different.  
Something else.  With those digital where the entire electronics goes inside the incubator, I've had the readings go wonky in the higher humidity.  Talk about nerve-wracking late in a hatch.
I can't explain what if going on with yours with those big temperature swings.  If it were a still air, it could easily be explained, but not a forced air.  
If the temperature is really truly 99.1 instead of 99.5 in a forced air, don't be surprised if your hatch is late, maybe even a day or more late.  They will develop slower if the average temperature is low.  But I'd expect them to hatch OK at 99.1 degrees.  How close to the 21 days they hatch is a good indication of whether you need to adjust the incubation temperatures.  Better than an uncalibrated thermometer for sure.
I don't know that I've eased your worries any.  I do think the best thing for you to do is be consistent with this hatch unless you do find something you know is wrong.
Good luck!