First of all, in a two needle, four thread serger, the two needles DO sit at different levels so this is correct.
The looper threads are knitted into the needle threads as the stitches are formed so these threads may appear to "change places" depending where you are in the stitch cycle when you stop the machine.
My machine skippes stitches like this if one of the needles needs to be replaced (because it is dull or just ever so slightly bent) so try replacing the needles.
If this doesn't work, then it is likely that the looper timing is off. I know you say that you "checked the timing of the upper and lower loopers and the needles" but your question regarding the height of the needles suggests that you are still fairly new to sergers.
If you are only missing loops intermittently, the stitch will still function adequately if all you are doing is finishing seams or making T shirts.
Good luck.
PS
Sorry, I don't know of a web page that has detailed information regarding setting the timing for sergers. I found this site while searching for such a page!
J Korte
April 2006
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