Caincad - We exprrienced this same problem and found the solution right here in the Eng-Tips web site. If I understand your problem, the number of layers in your drawing has exceeded the limit set in the "maxsort" systen variable. To get your layers to come up alphabetized, type "maxsort" at the command line and change the default from 200 (I think) to something like 500. This has taken care of 99% of the drawings we have come across.
Good luck. Hope it works for you.