As an alternative to mastic-type goo you could try EPDM dry glazing tape, such as that stocked by ironmongerydirect.com. This is a dense foam rubber self-adhesive tape which is aplied to the rebate to form a gasket. I use it to install double glazing units in timber frames (on land!) and have had good results. It's a lot quicker and cleaner than mastic, and it remains flexible over time.
If you do go down the mastic route I'm a fan of polysulphide sealants, such as Arbokol. One common cause of failure with mastic seals is squeezing the joint up too tight on assembly. If the mastic film ends up too thin then the material can't accomodate the shearing forces involved due to differential movement, and the joint fails. It's important to design in a suitable thickness of material - this might involve creating a groove in the rebate to contain a bead of the mastic.