find this from about ten days ago:
Pakistan accepts India’s offer, appeals for more aidForeign Minister Qureshi told India's NDTV television in an interview broadcast Friday that Islamabad would take India's offer of five million dollars which was made last Friday.
“I can share with you that the government of Pakistan has agreed to accept the Indian offer,” Qureshi said from New York, where he addressed a special session of the UN General Assembly called to boost aid for flood victims.
“I think this initiative of India is a very welcome initiative.”
India and Pakistan have made major efforts in recent months to build confidence in their relations, which were badly strained by the Mumbai 2008 terror attacks, which Indian blamed on militants from Pakistan.
The United States urged Pakistan earlier this week to accept the Indian offer and not let rivalry stand in the way of helping its citizens in flood-ravaged regions.
Indian Prime Minister Manmohan Singh rang his Pakistani counterpart Yousuf Raza Gilani on Thursday “to express his sense of sorrow and to condole the deaths resulting from the huge floods,” Singh's office said
The person mentioned in your link is a 'spokesperson' for the foreign ministry. But there is nothing in the words of the Foreign Minister himself to say that there were any conditions for the acceptance of the money.
It is possible that they asked the UN to manage the money as they are most likely sensitive to being accused of using the money, as the previous administration did, for the military eg.
But these words from the Minister seem to indicate that Pakistan is very grateful for the offer of help. Sometimes spokespersons say things they should not, hopefully that is what happened.