There are two things here that I found out that may help people.
To the OP, there are three penalties for underleveled weapons. They take more damage from higher level mobs, the miss more, and they do less damage. The last two cause a 4th problem in that they have a slower skill gain.
As for the issue with the phantom skill ups. This appears to happen after SE changed the log so you now only see your skill and Exp. You still get the skill (unless a party member is in a different zone). The cause appears to be related to non-mob related abilities triggered at the time of the mobs death. Either way if you check your stats you will still have gained the exp. It just doesn't show it.
I've seen skill up in log during battle. Not been shown tallied skill up at end of battle. And my skill points remain the same after battle is completed. ie: 1000/2200 before battle || skill during battle with no tallied result at end || 1000/2200 after battle.
Im sorry but I have seen your statement to be false.
I have heard of people not showing skill point tally at the end of a fight due to mob death via shockspikes or DoT spell. They however have points being added to their total rank points towards rank up.(Sorry I know that wording is horrible) - But that is a different glitch. Edited, Oct 6th 2010 11:07am by edge1006