What might have exactly caused Malegaon 2006 bomb attacks?

It was nothing short of a direct frontal attack. That too, a revengeful one. A group of Muslims had foiled the attempt of Swami Aseemanand to reconvert the Tadwi Muslims of Akkalkuwan and Navapur tehsils of Dhulia district as well as Jalgaon mofusil areas in Maharashtra that touch upon the Dangs of Gujarat.
Some extremists had systematically and stealthily changed school leaving certificates of Hamida Mohammad Tadvi. She was enrolled in Prathemic Vidyamandir in Kolhe village of Pachora taluka. Her caste and religion was entered as Hindu Tadwi Bhil. Like her Shamsher Kalu Tadwi, Musalman Tadwi Bhil; Hasan Murad Tadwi as Bhil, Prathamic Vidyamandir, Atalgahva, Jalgaon district; Sahamshad Mohammad Tadwi, Hindu Tadwi Bhil, Prathmic Vidyamandir, Kolhe, Pachora; Taslim Shamsher Tadwi, Hindu Tadwi Bhil, Prathmic Vidyamaner, Kolhe, Pachora, etc. Some of them were invited to the Shabri Daham Kumbh Mela (the brain child of Swami Aseemanand) on February 11-13, 2006. It was a showpiece for the gathering of 8 to 10 lakh Hindus. Arrangements were made from the fund collected by Aseemanand to transport them to the site of Shabri Kumbh Mela near Pumpa pond. They were meant to be reconverted.
But some Muslims got the wind of what was happening to their fellow religious rural folks. They visited the region on February 5 and dissuaded the Tadwi Muslims from attending such a ceremony as they were really Muslims and nothing else. This compelled the organizers of Shabri Kumh to cancel the special ceremony of welcoming the Muslims to Hindu fold. However the gathering went ahead with much fanfare, attended among others the chief of the RSS, Hindu religious leaders, activists of VHP, Abhinav Bharat, Jai Vande Matraum and others. Many noted people attended the gathering, among them was Sadhvi Pragya Singh Thakur. She was so close to the swami that on her arrest he simply went into hiding. Only in November of 2010 was he arrested from Haridwar.
In the follow up meetings in March 2006 and in other meetings Aseemanand, Indresh Kumar, Pragya, Lt Col Shrikant Purohit, and others met and decided to bomb Muslim populated areas of Malegaon, Hyderabad, Samjhauta express, Ajmer shrine. Their aim was to cause maximum casualty. Malegaon 2006 blasts achieved the target (thirty seven killed and 200 injured), and then the Samjhauta express bombing went beyond and killed 68.
To forestall the Tadwi samaj members from attending the Shabri Kumbh, Adivasi Unnati Mandal of Pahur in Jamner taluka of Jalgaon district organized a get together on February 5, 2006. Among its objectives was awakening of the downtrodden Tadwi Bhil Muslims, and giving them social, economical, educational and religious protection. The organizers also evinced that the downtrodden were coerced by other religious groups (to join them by abandoning Islam). They assured the people that the whole samaj is with them. A handbill signed by Ahmed Burhan Khan Tadwi of Haripura, Yawal, Gujarat, Masoom Rahim Tadwi of Maharad, Chopra and Ramzan Sardar Tadwi of Palan Taluka, Rawer was circulated towards achieving the above objectives.
However self defending in intention but this was perceived as a provocation. And as in the case of Babri mosque demolition, the right wing extremists made it manifest that the Muslims had it coming. This is clear from the meeting organized in Sangmeshwar, Malegaon on the eve of the bomb blasts of September 8, 2006. That public meeting of Jai Vande Matram on September 7, 2006 saw the police in induced slumber. It was a Rip Van Winkle sleep from which they have not yet woken up after more than four years. The nine Muslims who were made to bear the cross are still languishing in prison!