If you know the conflict is caused by the theme, the best advice would be to no longer use that theme. If you really want to use that theme, contact the theme developer and let them know about the problem and see if they can fix the theme for you.
Blubrry's development team strives very hard to ensure that PowerPress conforms to all of the current standards of WordPress. Sometimes, theme developers don't keep up with these standards, especially if it's a theme that's older and hasn't been updated recently. So, the theme may wind up causing conflicts because it's no longer in line with WordPress requirements.