You gotta low pitched, kinda groan sound coming from your brakes when your release them?
thats either brake dust, or out calipers not being lubricated properly, causing it to drag a bit. Check the brakes out, as it is most likely not the transmission.
Oh, BTW, you don't have racing brakes do you? they make all kindsa funny sounds when not warmed up, as the pad compound is really hard when cold.