I wouldn't diddle withe the magazines, you risk making them worse rather than better, I'd just go try some new mags. Wilson Combat and Tripp Research Cobra mags are the top two in my opinion.
As for the mag, you mean that when you load a full magazine, chamber a round, and them remove a magazine that the top cartridge (this would be the #2 cartridge) is loose, and that the #3 cartridge is now on top? Or are you topping off the magazine to refill it after chambering a cartridge?
If you download the magazine (load one less than full capacity) does it do the same? When the mags are new, and fully loaded, the mag spring is putting a lot of tension on that top cartridge and when the slide is chambering the #1 cartridge, friction from that top cartridge moves the #2 cartridge to some extend, ranging from just a little to all the way out.
I'd probably order some new mags. In the mean time, work the magazine spring by loading and unloading the magazine a couple dozen times. Leaving them loaded really doesn't work the spring but the repeated compressing / relaxing of the spring will.