I have a couple of custom DialogPreference implementations floating around, such as this one:
package apt.tutorial;
import android.content.Cont
I tried your code on the emulator. There is no problem with the code that you have given, and all the lines have the same formatting; but they all look more similar (in format) to the third preference (Lunch Alarm Time) than the others.
It looks like the other three preferences are getting indented more than required. So, maybe you have some global formatting style that is used, but not picked up by the TimePreference preference.
EDIT: OK. So, the above is not (completely) true. There is definitely a problem when I tried with the target sdk set to HoneyComb. But on setting the theme for the PreferenceActivity class as android:theme="@android:style/Theme.Black", there is a consistency in the look of all the preferences as shown below.

This style looks similar to Froyo, but not the HoneyComb; in the latter, the title font is smaller and there is more indentation. Probably, the default theme is not being assigned to Custom Preferences - just a guess :) A workaround would be to assign the default theme to your preference activity explicitly, but I don't know what the default theme in HoneyComb is (and whether it can be set).