I've noticed that the durations and/or effects of Magic Weapon and Greater Magic weapon are erratic, at best - especially when fighting chosen.

1) In several instances, I have not managed to get past the Chosen damage resistance even when my weapons had a +1 Enhancement bonus from Magic Weapon (or +2 from GMW). This has applied to normal Chosen, Greater Chosen, and Chosen Hunters randomly.

2) In several instances the Magic Weapon and Greater Magic Weapon spells last only a couple of rounds, or turns, or much shorter than their duration in the spell description. At other times they even outlast some of my other 1 hour/level spells.

3) When other weapon enchantments, such as Flame Weapon or Keen, fade from weapons on which they have been cast, there seems to be a risk that the weapon is stripped of all enchantments- or at least Magic Weapon or GMW enhancement bonuses; or that these stop working (according to point 1).

To address number one, make sure you are using the right tool for the right job (or in this case, right enchantment for the right enemy). Not all chosen hides share a uniform hardness, meaning some chosen types may be more difficult to penetrate than others.

To address number two, I would make sure the spells you think are supposed to be lasting an hour/level really truly are supposed to be lasting that long. We've made a number of changes to spells on EfU which can be found in the mechanics changes guide and some of the changes include lowering the duration of some spells like Stoneskin.

Not really sure how to address number three. I've heard of similar issues being mentioned before, but don't remember it ever actually being a bug. Maybe another DM has something to say about it.

To address number one, make sure you are using the right tool for the right job (or in this case, right enchantment for the right enemy). Not all chosen hides share a uniform hardness, meaning some chosen types may be more difficult to penetrate than others.

I am aware, and have. It is still erratic. Tests against Chosen Hunters give me that, at times, I need a +1 enchantment to harm them, at times a +2 enchantment, and at times neither work. It is in the same spawn point, in the same area. This goes for Greater Chosen and others as well. Note also that once it stops working against one type of Chosen, it stops against all types of Chosen (and often fades directly after, even though I cast it just a minute before - and unless they last 1 round/level should still work).

We've made a number of changes to spells on EfU which can be found in the mechanics changes guide and some of the changes include lowering the duration of some spells like Stoneskin.

See above. They often last for only a couple of rounds, which is shorter than intended. Not often enough to make it instantly deadly, but often enough to make it a serious issue.