I always figured it like this:
In GGGoH, Clark had never been exposed to green K before. So he had no tolerance to it yet. So, when he was exposed, it knocked his powers offline for a day before he recovered.
He really doesn't have any exposure to it again until HoL, where he is stuck in the cage for at least several hours. At this point, he's been exposed to it before, so he's developed at least a small tolerance to it. BUT, it starts to drain him...like a battery. When Clark is finally free of the cage, his battery automatically starts to recharge. He spins into his regular suit, but that's all he's got left in him. When Luthor jumps, his battery is once more drained. Hence the "I can't" comment - he literally can't save Luthor because he's completely powerless again.
By the time of ME, he's had a considerable amount of exposure to green K. (A couple of times in GGGoH, thanks to Jonathan and Trask, and several hours worth in HoL.) So his tolerance level is much higher. Hence, a basically instantaneous recovery once the bullet is removed from his shoulder.
Red K is a different beast. It has the same basic properties as the green, but is different enough that it not only affects him physically in different ways (apathy, steals his powers, makes his powers go haywire) but also has variable duration times, though it seems like in all the above cases, his recovery is never instant - it lingers far longer than the effects of green K.
