The Planar Shepard is well known as the most utterly broken PrC. I have no idea why your DM would allow it, unless the other players are an Archivist, a Artificer, and an Incantatrix. And even then, nothing they do can compare to the Planar Bubble.
Unless I'm miss-remembering, Planar Bubble is a Supernatural Ability (Su). Supernatural abilities are magical and go away in an antimagic field but are not subject to spell resistance, counterspells, or to being dispelled by dispel magic.
Thus, once the Shepard creates a bubble, you lose unless you can cast Anitmagic Field.