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I'm trying to set up two list boxes, one for the user to select the year, the other to select the month. My input data includes a date-time field called evttime. I set the expression for these boxes to show year(evttime) and month(evttime) respectively. When the user selects a year, say 2017, the months Sept, Oct and Nov are automatically being selected. Any idea why this might be happening?

That is the power of Qlikview Associative concept. When you selected the "Year" in the list box it will automatically shows the months that are related to the year. So when you selected 2017 it is showing the months that belongs to the year 2017. Google and see about "Qlikview Associative" and learn.
There might be a trigger in your document. Just go to doc properties using Ctrl+Alt+D -> Select Triggers tab then look for your month field if you have any triggers. OR got to Sheet properties Ctrl+Alt+S and look any triggers enabled for this month field.
I understand that this is why I only see Mar - Nov as selectable fields, since there is only data for Mar - Nov in my data set. It doesn't explain however why the months Sep, Oct and Nov are highlighted in green, as shown in my screenshot.
One thing to note: even though Sep - Nov are "selected", other charts in my documents are not being filtered to just these months, they are showing all data available for 2017.
No triggers have been set, on any field.
Would you mind sharing your app here to look into. You can scramble any potential data using scrambling technique.
Preparing examples for Upload - Reduction and Data Scrambling