Yes, it's a bit like that... 'en' words are called common gender (Swe: 'en-ord' or 'utrum' or 'reale'), and 'ett' words are neutral gender (Swe: 'ett-ord' or 'neutrum'). The common gender is a fusion of once existing masculine and feminine genders, a simplification that took place in the late middle ages (the three gender system remain in a couple of very special dialects with few speakers, though). 75-80% of all nouns are in the common gender but unfortunately there are not a lot of rules out there to make it easier to decide if a word is an en-ord or ett-ord...
Well, for learners of the Swedish language it indeed does sound as if the stress was on the last syllable. So far the same goes for "kvinna" and "flicka".
The reason for this is the so-called accent 2 (at least in German it's called like this), which is also existent in Norwegian (only in part?).