The SICK Stegmann Hiperface SEK/SEL series encoders have the lowest incremental resolution of all Hiperface encoders at only 16ppr (64 counts). This makes the Electronic Alignment tool much less accurate and you may notice angles being set far off from the angle you entered, especially on motors with a high number of poles.
If the encoder is used on a Rexroth MSK series motor, then the better option is to use the Rexroth MSK Memory Programming to write a new angle into the memory data that matches your current alignment. If the encoder is not on a Rexroth MSK motor then you will likely need to use the following technique. We are working to develop more support for these encoders, including the ability to run from them.
They can be aligned correctly by using a combination of mechanical adjustment and electronic alignment. Simply try aligning the encoder using the electronic commutation tool. If the angle is off then remove the center bolt from the encoder, jiggle the disc into a new position, then re-tighten and try electronic alignment again. Eventually the disc will be in a good position where the electronic alignment should fall within our 3 degree tolerance.
Video of the electronic alignment process: