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The genres are different. Om Shanti Om tilted more towards comedy, while Welcome was a non-stop laugh-riot. Both were mass-friendly films. Jodhaa Akbar is a historical and generally speaking, history is not everybody's favorite subject.
The release period was different. Om Shanti Om opened during Diwali, while Welcome was timed during Christmas vacations. Jodhaa Akbar didn't coincide with any festivities.
In India, Om Shanti Om was released at multiplexes and single screens at one go. Welcome had a Friday noon release at multiplexes. Jodhaa Akbar lost out on the Friday booty since UTV and the multiplexes couldn't reach a settlement till Friday night. Resultantly, Jodhaa Akbar opened at several multiplexes across the country on Saturday, but the moviegoer was completely clueless of the development. It was only towards Saturday noon/evening that the multiplexes started reporting better occupancy.
Jodhaa Akbar didn't release in Rajasthan, thus losing out on a substantial amount.
While four shows a day were performed at single screens for Om Shanti Om and Welcome, in this case, the shows were limited to three shows a day, looking at its excessive length.
The budget of the film was initially Rs. 37 cr., which shot up to Rs. 40 cr. Add to it another Rs. 8 to Rs. 10 cr. for print and promotion, which takes the final cost to Rs. 48 - Rs. 50 cr. And that amount is a cakewalk given the business at multiplexes of India, Overseas and also sale of Satellite and Home Video rights. In fact, the film should fetch an astronomical amount from Satellite and Home Video territory. All said and done, Jodhaa Akbar is, in terms of economics, a success story. Pessimists be damned!