We have been experiencing the exact same thing and not just with the Intensity but with the DeckLink SDI as well. Everything is flawless for the first couple of minutes and then drops down to 5-10fps.
I suspected that perhaps the input processing of these cards may have something to do with this, especially the Intensity’s, as afaik its done in software (and the DeckLink’s in hardware?) but ruled this out as even with 480i input the same thing happens.
Btw, I can confirm that 1080i/720p input works in FMLE 3.1 (which isn’t out yet but I’m a beta tester), however it doesn’t mean much with these horrible frame drops. An FMLE developer in the Adobe beta forum mentioned that these issues may be due to a problem with Timestamps. I do not know how this carries over to the Windows side of things as DirectShow and QuickTime are two different animals, but it’s worth a mention.
I would really like for someone from Blackmagic to shed some light on this. Thanks in advance!