Yeah, I agree it wasn't consistent. I believe S1 affects were longer, he was really exposed twice in this season. The first time was from a huge chunk, which could explain the long duration of being powerless. The brief exposure from Mrs. Cox's necklace wasn't hands' on so it doesn't really count. In the cage he had both REALLY Long AND hands on exposure (the number of times he grabbed the cage).
When I first time I saw HoL on Netflix's Instant List, the whole wedding / cage scenes (like 15 minutes of it) were missing. So, I never saw how Clark freed himself from the cage or how long he was in there. I had to guess and make assumptions of what really happened (until I bought the DVDs). I thought Clark made a conscious decision not to save Lex, (a) because Lex didn't deserve it, and (b) he had Lois in his arms and if he went to save Lex, everyone would know CK=SM, which meant saving Lex wasn't worth revealing his secret to the world and ruining his own life. It made more sense in Madame Ex why everyone turned against him (i.e. Clark's guilt trip). The main reason I figured Clark had his powers back during Lex's death fall was that Clark was once more dressed in his business suit. If he was able to spin into / out of the suit (or fly/run home to change), then I figured he must have had his powers back already.
I hated how the Kryptonite exposure hardly affected him(although the characters said he was weaker afterwards) in Madame Ex. It's a poor way to start the second season, IMO, by changing the rules (and Jimmy, but that's another pet peeve for another thread). Having just watched Madame Ex again recently, I agree. It doesn't make much sense to have him writhing on the floor, probably dead within minutes but still able to use his heat vision.
This doesn't work especially if compared to Ordinary People, where he is exposed to Kryptonite *doesn't* feel the pain, but ALSO only notices the exposure due to his LOSS of heat vision. It also doesn't make sense when compared and contrasted with the the Kryptonite bullet. How could the kryptonite bullet penetrate his skin in Madame Ex, but it takes prolonged exposure to weaken him enough in Ordinary People for surgery?
I've been reading some Superman ShowCase books (which has some of the main stories from the 50's-60's comics) and the story I read last night had Clark near death's door due to exposure to Kryptonite but then okay again (with full powers) as soon as it was taken away.
In my stories, I play around with how long it takes Clark to recover based on length of exposure, type of exposure, the amount of Kryptonite used, and.... plot.

Hey, if they can use that excuse, why can't I?