The two 2496 units should be sync'd together. Doing this will change a few things, primarily, your digital output options.
Now, if you sync the two 2496 units, you run them into each other, and just pick one and set it to external sync, the cards would be fine.
My question is that if you do this, what outputs are you going to be losing? You have the two RCA on each card, that could give you one stereo input, and you could set one to drive your monitors. Alternatively, you could run the one that you pick for output into the DacMagic using RCA, and run that out to your monitors, etc as wanted.
This would remove the MyTek from the mix completely, and that's where I believe the problem lies. The sync just isn't with the right units.
Feel free to entertain the idea, or try to tell me why you want to run things a different way, I ran two Delta 1010's with world clock until I moved to a 1010AI box, now I am yet to set up the S/PDIF sync for full use, since I'm not usually recording with all the cards at once, I don't have a clock problem right now...
Core 2 Quad Q9400-Scythe Ninja Rev A|MSI Neo P45|WD 150GB Raptor|WD 250gb SATA-I|8GB G-Skill DDR2|WD Blue 640GB SATA-II|Logitech KB|Apple Mighty Mouse|ATI HD4850 512MB-Accelero S1|M-Audio 2x Delta 1010|Delta 66 Omni I/O|Corsair 400W|Cooler Master Elite 330
Dual Boot: Ubuntu 10.04 x64 Lucid/Windows 7 Home Premium x64
Adobe Audition Mac & PC, Logic Pro, Ardour, PT 9, Reaper x86 & x64, Ableton Live Lite
2x Delta 1010, 2x Delta 66, AP2496, FW Solo, Pulsar II, ProFire 2626, Fast Track C400