The MDX times come directly from the attraction wait clocks. The third party app estimates the times or uses crowd source information, which can be very variable in frequency and accuracy.
This is unfortunately a big problem with Windows phone right now. It has such a small market share that many app developers do not have the time or budget to make development for Windows phone worthwhile.This is upsetting - I can not even use MME APP because I have a Windows phone.
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