That is normal for low resolution monitors. The flicker comes from interlace, i.e. the monitor updates at half frequency (sort of).
You can't remove the flicker for the windows desktop but you can reduce it by:
- make everything bigger vertically, e.g. use a larger font, increase the window borders (display properties/appearance/advanced) etc.
- Reduce the contrast. e.g. make the bakground black and the font grey.
For best result you should look into a mame frontend instead of using mame32.
For the games you can remove the flicker by turning on "cleanstretch vert" for horizontal games and "cleanstretch horiz" for vertical games (or use "cleanstretch full" for all games but then some games will have the wrong proportions).
For best results you should define custom resolutions for the games.