First, the "slow pulse" trackball notification is tied to HTC Sense. That's why you see it in Sense ROMs and not on others. I have no idea if it's possible to speed it up or anything, but I'd imagine it would be difficult to figure out, considering how difficult it seems to be modifying many things within the Sense framework.
Second, my trackball lights up on any notifications I want it to with xtrSENSE4.6, so I can't reproduce your issue. I have it light up for missed calls and SMS/MMS. I can also have it work with e-mail and Facebook, although I keep those notifications Silent without any help from my trackball.