StratixIII EPCS problem VCCSEL?

I hear some confusion from your post, I think, you may want to read the Startix III hardware manual more thoroughly. The basic point with AS configuration scheme is to provide a correct VCCPGM supply, with Altera EPCS devices, it has to be 3.3V. The bank containing the DATA0 pin should have at least a VCCIO of 2.5V, otherwise some means of level translation, e.g. a resistive divider would be necessary (not an Altera suggested solution, but should work anyway).