I think you may be mixing issues here (and I'm confident others will straighten it out)
The capital gains exclusion is $250,000 per person, so if you file Joint it is $500,000. Filing Separate it's $250,000 for each taxpayer. If you sold 2 homes this year, the maximum exclusion is $500,000 - not $1,000,000. There is no advantage to filing Separate to somehow increase the benefit that I am aware of.
can you please add some dates to each home situation? it'll help others explain the capital gains situation. @Carl
Home #1 - when did you buy (month / year) ? when did you get the PCS orders (month / year) ? when did you rent (month / year) ? how many months did you live in the home since you purchased it?
Home #2 - when did you buy (month / year) ? when did you get the PCS orders (month / year) ? how many months did you live in the home since you purchased it?
