During the Musharraf era, on the United States pressure, Pakistan long ago abolished the Lashkars and the Jaishes and they were out of the power structure. They were there in the first place, because it was ironically also the US pressure to have its fight been fought in the Afghanistan. It was also thought that they would act as an army of US in disguise of regional force in South Asia.
All that was scrapped and forgotten and when the blow came after 9/11, all these militants organization were banned and they were hidden then. Some became focussed unsparingly but unorganized way on Kashmir and some went to Afghanistan. What else were they expected to do? They were forgotten and they were expendable for the US and yes for the Pakistan.
Now after Mumbai blasts, the thing is that the focus has once again diverted towards these non state actors which are Lashkars. The perception in India is that these are involved in the attacks and an offensive was launched in India. The response was negative and it only muddied the waters.
Allegations and cover-ups are not the solutions and both India and Pakistan must see through the smoke screen.