Royal Mail need to keep franked and stamped mail seperate for sorting reasons - especially since Pricing in Proportion came into effect in late August.
Most companies received new franking machines, which automatically weigh and measure the envelopes and will adjust the price accordingly, these letters can be sent straight out. Whereas they still have to check stamped mail as someone may have misunderstood the new methods.... Either way, if you put it in the franked mail box it will still get there... Dont' put too many in, as they can return them to the sender!