My two drives are currently operating fine under AHCI, so I suspect my problems were down to buggy Intel Matrix drivers.
Since I disconnected my eSata drive (rather thasn just turning it off), the odd IMSM pop ups about a new device have ceased, so I guess they were down to it partially identifying the powered down drive (another Samsung in an IcyBox enclosure), though I don't even know if that's electrically possible. Certainly another unexpected oddity which doesn't instill confidence in driver robustness.
I won't personally be using Intel Matrix Raid again, ever, unless it's in a hardware set up which has been explicitly stabilty tested wrt a particular driver version & I can't see myself ever having the time & inclination to do this, as these problems took months to become apparent.