I've run into this as well. Likewise I find that some white/cream pants allow underwear to show through (at least darker colored boxers). My solution has been to just keep shopping around....I find that cucinelli pants are typically opaque.
I recently purchased a few pairs of EM for Mason's (red, khaki, creme and white) and have been very pleased with them. Neither the creme nor the khaki seem to show the pockets and the pants are quite reasonably priced for well-fitting business casual workhorses.