While not having the problems you described with no notification at all, I do have the problem of the slow blinking frequency, which directly started after the Update 1.2.8.
I already asked in another thread but no help until now (see below).
I noticed it with the messanger Conversations (see link below) and I noticed it as well with the app "Prof. Reminder": the LED isn't influenced by the pulse length settings.
And additionally to a very low frequency of blinking (~once every 3-5sec, disregarded the settings), the LED is just slowly rising, instead of a real, digital "blink" (as it was for sure before the update to 1.2.8 for the Conversations notification....
Can anybody bring light to this behaviour?
I have rooted the phone (and used the updated boot.img) and have GravityBox running.
Link to my other post about this: