I managed to recable to get the Gefen switch out of the loop. This unit definitely has more sync problems than my 37w1 did, but so far I'm still thinking it's acceptable. (I'm also thinking I can make these problems all go away as soon as the Crystalio II can be bought here, but I realize that's not an option for most people.)
For example, in pretty much all configurations, when switching to an SD channel I very occasionally see VBI data at the top, but an off/on cycle of the source cures it. Very occasionally when switching to a 720p source the whole image is shifted down and to the right, again cycling cures it.
With the Motorola 6412 (phase II, DVI out), on all three digital inputs, when the 6412 is displaying 720p content at 1080i output (meaning, the 6412 is doing the 720p->1080i conversion), there's a misplaced-and/or-rotated-or-something line or two at the top of the screen. Disappears if I switch the 6412 to output 720p (which I usually take the trouble to do anyway). Never saw this on my 37w1.
Good news (for those that don't use a Gefen switch): with the Gefen switch out of the loop, HD content on DVI2 no longer has the vertical area of garbage on the right side of the screen. Never saw this kind of problem using the Gefen switch on my 37w1.
With the Sony DVR (HDMI out) connected to the HDMI input, I get fairly frequent handshake problems when switching channels, sometimes failing to lock. There's an audible click at each retry (even with sound off/muted). I tried two different cables. No handshake problems on either DVI input.
With the Sony connected to DVI2, with 1080i HD content there's a garbage line at the bottom of the screen that I don't see when connected to DVI1.