I had the same problem on my old laced boots (gone to speed lace now)
Sometime ago some posted a great description on how to tie laced boots.
If I remember, there were 2 ways.
Basically at every hook, pull, tighten and either:
a) hook over the top of the hook, coming out the bottom. Like wrapping the loop around the hook
b)hook them in the bottom of the hook, spiral the laces once around each other and repeat.
I used the second method and the problem went away.