Why are military ranks so often pronouced differently from the way they are written? Is there something specific about the history of these terms that makes it so?
Nothing special, but the words tend to be very old and passed along from French.
Just another example of our wonderful language.
Your question is just a general statement the probably is of private interest to you. 
It isn’t a major offense and doesn’t require corporal punishment. :eek:
Colonel is the only one I can think of with a major difference between spelling and pronunciation.
What others is the OP thinking of?
Colonel and Lieutenant were the ones I had in mind.
Lieutenant. Pronounced leftenant.
Although I believe the Americans pronounce it lootenant.
Though in America we pronounce that one correctly. ( 
)
I believe Cecil has covered Colonel at some point. Ah yes, here it is.