Hi Steven,
I have been using MA6 mask aligner for some time now. There are 2
programs for proxy exposure a) Proxy 1 and b) proxy 2. My guess is
that you are using proxy 2 where the substrate and the mask come into
contact with each other for WEC and after the WEC happens the
substrate goes to the alignment/exposure gap. Hence in Proxy 2 the
substrate and the mask are in contact with each other. In proxy 1, 3
flags will come in between the mask and the substrate and hence a
contact between them is avoided.
You can use the proxy 1 exposure only if your substrate is of the size
of the chuck.
Please be informed that WEC happens only once (i.e the first time) in
proxy 2 and the rest of the exposures there is not WEC. The substrate
directly goes to the alignment exposure.
If you see some beads on the edge of the substrate you can use a
suitable Edge bead remover (thickness of the beads can be
considerable). My guess is that the photoresist sticks on the edge of
the mask and not in the center. This could be because of the beads.
Thanks,

Dr. Sudesh S Bhagwat,
Group Leader,Substrate Processing group,
Samtel Centre for Display Technologies,
Indian Institute of Technology Kanpur,
Kanpur - 208016. INDIA
Tel:+91-(0)512-2596088
Fax:+91-(0)512-2596089