I would try turning off double screen size, and setting MAME to a low resolution (below 300 vertical lines). Also, I would try changing the triple buffering settings.
As for using a HDTV, I would try setting it to 480P or 720P and see what happens. The "Progressive Scan Modes" are not interlaced, and therefore less flickery. Modes than end in an i (480i, 1080i, etc) are interlaced, and more flickery. The other thing is that some HDTVs are 16:9 ratio, which would probably look bad in MAME for many games. However, some games (such as CPS2 games, are essentially 16:9, and would look very good on a 16:9 TV. There are commands in MAME to force the aspect ratio.